Why did the Gemara question whether Chamor No'er etc. is the beginning, middle or end of the Mishmar? Let's listen to the Chamor, and then we will know!
To set the records straight, the Gemara does not suggest that Chamor No'er takes place in the middle of the watch, only either at the beginning or at the end.
In answer to your question, I do not imagine that at the exact moment of the respective Mishmaros (whenever they occur) all the donkeys suddenly start braying, all the babies start feeding and all the women start talking to their husbands. Clearly, all of these are merely a rough a guage (indeed, the Gemara refers to them as a 'Siman' and nothing more).
Consequently, it is possible that one or two donkeys do not abide by the rules and starts braying earlier or later, and it is only the majority who bray 'on time' (and what about donkeys that are sick, that are giving birth and that are dying?). It is also possible that they start braying at the beginning of the first Mishmar and finish at the end, leaving us with the two sides of the She'eilah.