After Bem swaps the communicators for fakes, Kirk is shown using his as if it were his usual communicator.
When Bem was escaping the wooden cage by splitting into pieces, the bottom half of his body was shown walking out of a big hole in the cage. This hole was not there and that size piece of body could not fit through the existing holes. Also the cages were just on the grass with no bottom, so any of them could have just lifted them up and got out by themselves.
Kirk maintains an eye on Commander Bem among the aborigines, fearing against permanently losing track of him otherwise. This doesn't make sense. Commander Bem is a unique species in the area. It shouldn't be hard for the Enterprise to locate him in the relatively small area.
Lt. Arex, instead of looking into the beam down area first, searches the entire planet for Kirk, Spock and Bem.