Maybe your wife did this, and maybe your son has this perception that is not entirely accurate. No one can say because unfortunately your wife is no longer here. What's damaging though is that your son has carried this resentment with him and has never spoken of it to you. Do you have any idea why?
There's nothing you can do about it now except to have your son, and yourself if this is bothering you, go to counseling to sort through some things. It may be that there were some indicators that you didn't recognize. Maybe your daughter didn't see it, maybe she did and won't discuss it. But a lot of emotions arise - and resentments too - after a death when people feel free to talk and let go of some deeply-held feelings or even secrets.
Without knowing what other issues are at play here, and without knowing the nature of the mistreatment, it's hard to advise you on how to advise your son. But counseling is always a good start when there are unresolved problems, hurt and anger.