"Why do you not respect your mother?"
Translation:Dlaczego nie szanujesz twojej matki?
The first and third examples - I know what you're talking about, but it works differently because the object is a pronoun. We teach to avoid putting any pronoun (or adverb, by the way) at the end of the sentence, if only it's possible. In those sentences it's very easy to find another place. If they were about "your mother" instead of "her" or "you", they would simply be "Ten kot nie lubi twojej matki" and "Ona nie widzi twojej matki".
You can read more about it in Part 2 here: https://forum.duolingo.com/comment/28029344 The second example, "Jaki chleb lubisz?" - I don't see how it's relevant here, I'm afraid.