There is nothing bad if you say thank you to your mother-in -law after meal. Because here in our home, it is a norm to say thank you to our elderly ones( my parents) and guest after meal. Even if she assisted or not saying thanks to her is not a big deal, it is a sign of respect. Even my siblings do say thanks to me after meal in the presence of my parents. It is a norm like I have said, so you shouldn't take offence with what you wife said. It may be how she was trained that was why she confronted you. You should also see your mother-in-law as your own mother.