Chang could be upset about the two bunnies, because any time you ring two identical entities from separate time-spaces together, there is the possibility for a paradox to occur, resulting in the complete collapse of the atomic structure of the universe, simultaneously completely rendering all matter non-existent. Including the entire planet earth, and every thing that lives. Miles being in the presence of his baby self isn't a paradox, but the fact that he is there opens up the classical paradox scenarios of killing himself as a baby, etc. The two bunnies appearing together wasn't a paradox, obviously - because nothing bad happened, but Chang was concerned about the potential of a paradox - if the future bunny shot the past bunny, for example - so he quickly ordered that the bunnies be separated and not allowed to see each other. Maybe? Just a thought.