How old is he? Maybe he just doesn't like the act of being changed? Have you tried making the routine a little fun that usual? Maybe playing with him will help. My baby used to cry after taking a bath because he really loves bathing, and he'd continue crying while being dressed. What I did was just play with him and now, he enjoys getting dressed too.
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How old is your son? My daughter cries everytime we change her clothes since she was 6months old up to now (10months old). I mentioned it to our pediatrician and she said that it's common.
It could be discomfort causing him to cry whenever clothes are put on and taken off. Maybe try to be gentler (if you haven't already)?
I'm not sure if that's bad, but that does sound unusual. If this continues, maybe have him checked by a doctor just to be sure.