What is the reason for fear induced defecation?
If your mice are stressed or scared during those manipulations, as we can expect them to be, defecation can be a consequence of the "Fight-or-Flight response": in this situation, the organism try to focus its energy to act quickly, and a wave of specific neurotransmitters (noradrenaline in particular) is released. In consequence, mice's bladders relaxe, which cause them to urinate, the digestion stops, but the transit of the faeces in the colon is accelerated: they defecate. 

This is all controlled by the activity of the sympathetic nervous system, which secrets acethylcholine and noradrenaline.