ﻣُّﺤَﻤَّﺪٌ ﺭَّﺳُﻮﻝُ ﭐﻟﻠَّﻪِ ۚ ﻭَﭐﻟَّﺬِﻳﻦَ ﻣَﻌَﻪُۥٓ ﺃَﺷِﺪَّﺁﺀُ ﻋَﻠَﻰ ﭐﻟْﻜُﻔَّﺎﺭِ ﺭُﺣَﻤَﺂﺀُ ﺑَﻴْﻨَﻬُﻢْ ۖ ﺗَﺮَﻯٰﻬُﻢْ ﺭُﻛَّﻌًﺎ ﺳُﺠَّﺪًﺍ ﻳَﺒْﺘَﻐُﻮﻥَ ﻓَﻀْﻠًﺎ ﻣِّﻦَ ﭐﻟﻠَّﻪِ ﻭَﺭِﺿْﻮَٰﻧًﺎ ۖ ﺳِﻴﻤَﺎﻫُﻢْ ﻓِﻰ ﻭُﺟُﻮﻫِﻬِﻢ ﻣِّﻦْ ﺃَﺛَﺮِ ﭐﻟﺴُّﺠُﻮﺩِ ۚ ﺫَٰﻟِﻚَ ﻣَﺜَﻠُﻬُﻢْ ﻓِﻰ ﭐﻟﺘَّﻮْﺭَﻯٰﺔِ ۚ ﻭَﻣَﺜَﻠُﻬُﻢْ ﻓِﻰ ﭐﻟْﺈِﻧﺠِﻴﻞِ ﻛَﺰَﺭْﻉٍ ﺃَﺧْﺮَﺝَ ﺷَﻄْـَٔﻪُۥ ﻓَـَٔﺎﺯَﺭَﻩُۥ ﻓَﭑﺳْﺘَﻐْﻠَﻆَ ﻓَﭑﺳْﺘَﻮَﻯٰ ﻋَﻠَﻰٰ ﺳُﻮﻗِﻪِۦ ﻳُﻌْﺠِﺐُ ﭐﻟﺰُّﺭَّﺍﻉَ ﻟِﻴَﻐِﻴﻆَ ﺑِﻬِﻢُ ﭐﻟْﻜُﻔَّﺎﺭَ ۗ ﻭَﻋَﺪَ ﭐﻟﻠَّﻪُ ﭐﻟَّﺬِﻳﻦَ ﺀَﺍﻣَﻨُﻮﺍ۟ ﻭَﻋَﻤِﻠُﻮﺍ۟ ﭐﻟﺼَّٰﻠِﺤَٰﺖِ ﻣِﻨْﻬُﻢ ﻣَّﻐْﻔِﺮَﺓً ﻭَﺃَﺟْﺮًﺍ ﻋَﻈِﻴﻤًۢﺎ

Muhammad (SAW) is the Messenger of Allah, and those who are with him are severe against disbelievers, and merciful among themselves. You see them bowing and falling down prostrate (in prayer), seeking Bounty from Allah and (His) Good Pleasure. The mark of them (i.e. of their Faith) is on their faces (foreheads) from the traces of (their) prostration (during prayers). This is their description in the Taurat (Torah). But their description in the Injeel (Gospel) is like a (sown) seed which sends forth its shoot, then makes it strong, it then becomes thick, and it stands straight on its stem, delighting the sowers that He may enrage the disbelievers with them. Allah has promised those among them who believe (i.e. all those who follow Islamic Monotheism, the religion of Prophet Muhammad SAW till the Day of Resurrection) and do righteous good deeds, forgiveness and a mighty reward (i.e. Paradise).
48:29

Ibn Katheer mentioned that;

Imam Malik used the verse as evidence that the shia are disbelievers, because of the part of the verse that says;

" ....He may enrage the disbelievers with them.."
tafseer ibn Katheer 7/362

Imam Qurtubiyy said;
Malik has done well in his statement and was right in his interpretation... (tafseer Qurtubiyy 16/297)

Ibn Hazm also said;
As for the claim of the rafidhah that the Quran was changed, then they are not muslims, rather it is a sect that was innovated 25 years after the prophet's death alyhissolaat wassalaam (Al fisal fil milal wa nihal 2/65)

https://islamqa.info/ar/113676

Undoubtedly it is a sign of great misfortune and misguidance if a person’s faith is based on slandering the companions of the best of mankind (peace and blessings of Allaah be upon him) or arguing about the disputes that arose among them, instead of occupying himself with doing that which will benefit him in both his worldly and spiritual affairs.

No one should have any reason to slander or hate or bear grudges against the companions of the Prophet (peace and blessings of Allaah be upon him). Their virtues are many, for they are the ones who supported Islam and spread the faith; they are the ones who fought the mushrikeen; they are the ones who transmitted the Qur’aan, Sunnah and rulings. They sacrificed themselves, their blood and their wealth for the sake of Allaah. Allaah chose them to be the companions of His Prophet (peace and blessings of Allaah be upon him), so no one slanders them or hates them except a hypocrite whose does not love Islam or believe in it.

It was narrated that al-Bara’ (may Allaah be pleased with him) said: I heard the Prophet (peace and blessings of Allaah be upon him) say: “The Ansaar: no one loves them but a believer and no one hates them but a hypocrite. Whoever loves them, Allaah will love him, and whoever hates them, Allaah will hate him.”
Narrated by al-Bukhaari, 3672; Muslim, 75.

If a man who hates the Ansaar cannot be a believer and that makes him a hypocrite, then how about one who hates the Ansaar and Muhaajireen and those who followed them in truth, and slanders them, curses them and denounces them and those who love them as kaafirs – as the Raafidis do? Undoubtedly they deserve more to be regarded as kaafirs and hypocrites, and of not being believers.

Al-Tahhaawi said, discussing the beliefs of Ahl al-Sunnah wa’l-Jamaa’ah:

We love the companions of the Messenger of Allaah (peace and blessings of Allaah be upon him) and we do not neglect to love any one of them, nor do we disavow any one of them. We hate those who hate them and who criticize them, and we only mention them in good terms. Loving them is part of religious commitment, faith and ihsaan, and hating them is kufr, hypocrisy and wrongdoing.

https://islamqa.info/en/45563

seems you've skipped something in the verse you quoted

Muhammad (SAW) is the Messenger of Allah, and
those who are with him are severe against
disbelievers, and merciful among themselves. You
see them bowing and falling down prostrate (in
prayer), seeking Bounty from Allah and (His) Good
Pleasure. The mark of them (i.e. of their Faith) is on
their faces (foreheads) from the traces of (their)
prostration (during prayers). This is their
description in the Taurat (Torah). But their
description in the Injeel (Gospel) is like a (sown)
seed which sends forth its shoot, then makes it
strong, it then becomes thick, and it stands straight
on its stem, delighting the sowers that He may
enrage the disbelievers with them. Allah has
promised those among them who believe (i.e. all
those who follow Islamic Monotheism, the religion
of Prophet Muhammad SAW till the Day of
Resurrection) and do righteous good deeds,
forgiveness and a mighty reward (i.e. Paradise).
48:29

Does the bolded show that some of the companions didn't believe in the prophet as it said "those among them who believe" or those it mean who you have bracketed ?

Let see what the koran says about some companions

[Quran 2:8-15] Then there are those who say, "We
believe in God and the Last Day," while they are not
believers. In trying to deceive God and those who
believe, they only deceive themselves without
perceiving. In their minds there is a disease.
Consequently, God augments their disease. They
have incurred a painful retribution for their lying.
When they are told, "Do not commit evil," they say,
"But we are righteous!" In fact, they are evildoers, but they do not perceive. When they are told, "Believe like the people who believed," they say, "Shall we believe like the fools who believed?" In fact, it is they who are fools, but they do not know. [/b]When they meet the believers, they say, "We believe," but when alone with their devils, they say, "We are with you; we were only mocking. "God mocks them, and leads them on in their transgressions, blundering.

Has this verse just signified that some of the companions had traces of hypocrisy?

Looking at the koran again

[Quran 4:141] [b]They watch you and wait; if you attain victory from God, they say (to you), "Were we not with you?" But if the disbelievers get a turn, they say (to them), "Did we not side with you, and protect you from the believers?" God will judge between you on the Day of Resurrection. God will never permit the disbelievers to prevail over the believers.

[Quran 48:11] The sedentary Aarabs who stay behind will say, "We have been preoccupied with our money and our families, so ask forgiveness for us!" They utter with their tongues what is not in their hearts. Say, "Who can protect you from God, if He willed any adversity for you, or if He willed any blessing for you?" God is fully Cognizant of everything you do.

[Quran 9:101] Among the Aarabs around you, there
are hypocrites. Also, among the city dwellers, there
are those who are accustomed to hypocrisy. You do
not know them, but we know them. We will double
the retribution for them, then they end up committed to a terrible retribution.

so do these show that some companions where hypocritical or do they mean something else?

Shaykh al-Islam Ibn Taymiyah said:

If a person slanders them in a way that does not impugn their good character or religious commitment, such as describing one of them as being stingy or cowardly or lacking in knowledge or not being an ascetic and so on, then he deserves to be rebuked and disciplined, but we do not rule him to be a kaafir because of that. This is how the words of those who were not regarded as kaafirs by the scholars are to be understood.

If a person curses them and slanders them in general terms, this is an area of scholarly dispute, depending on whether this cursing is motivated by mere feelings or religious doctrines. If a person goes beyond that and claims that they apostatized after the death of the Messenger of Allaah (peace and blessings of Allaah be upon him), apart from a small group of no more than ten or so individuals, or that most of them rebelled and did evil, then there is no doubt that such a person is a kaafir, because he has denied what is stated in more than one place in the Qur’aan, that Allaah was pleased with them and praised them. Indeed whoever doubts that such a person is a kaafir is himself a kaafir, because this implies that those who transmitted the Qur’aan and Sunnah were kaafirs or evildoers and that the best of this ummah which is described in the verse “You are the best of peoples ever raised up for mankind” [Aal ‘Imraan 3:110 – interpretation of the meaning] – the first generation – were mostly kaafirs and hypocrites. It implies that this ummah is the worst of nations, and that the first generations of this ummah are the most evil. No doubt this is blatant kufr, the evidence for which is quite clear.

Hence you will find that most of those who proclaim such views will sooner or later be shown to be heretics. Heretics usually conceal their views, but Allaah has punished some of them to make an example of them, and there are many reports that they were turned into pigs in life and in death. The scholars have compiled such reports, such as al-Haafiz al-Saalih Abu ‘Abd-Allaah Muhammad ibn ‘Abd al-Waahid al-Maqdisi, in his book al-Nahi ‘an Sabb al-Ashaab in which he narrated the punishments that befell such heretics.

In conclusion, there are some groups of those who slander the Sahaabah concerning who them is no doubt that they are kaafirs, others who cannot be judged to be kaafirs, and others concerning whom there is some doubt regarding that.

Al-Saarim al-Maslool ‘ala Shaatim al-Rasool , p. 590-591.