Fisher incorrectly refers to performing an "autopsy" on Ella. An autopsy is performed on human remains. The correct term for examining animal remains postmortem is "necropsy". This is a common mistake for most people, one that Fisher would not make, given his profession.
When he is being bathed by his mother, Allan Mann's arms and legs all have muscle definition. If Allan Mann was completely quadriplegic, this would be impossible.
In the scene where Ella's body hits Allan's tape deck, there's already blood on it before her body hits it.
(at around 1h 40 mins) Ella urinates on Allan as a sign of mating, but it's actually the male capuchin who urinates on its mate. This would suggest that Ella is in fact a male capuchin. However, this could be her way of asserting her dominance.