Repetitive utterances don't provide any new information about the child's language knowledge. If we include them, the MLU would tell us too much about the length of specific, frequently used utterances, and not enough about the child's range of expressive abilities. When children repeat an adult's utterance, they sometimes include segments that they haven't fully mastered. The adult's example helps them increase sentence length. The MLU should tell us about the child's knowledge not the adult's.
Unintelligible utterances are impossible to divide into morphemes.
If we include them, the MLU would reflect our guesswork. Answers to questions often build upon the question that was asked. They do not need to be full sentences. The more questions we ask, the lower the MLU is likely to be.