Water changes its scale at various times during the movie. Sometimes, it features surface tension consistent with the scale of the ants, then at others acts like water on the scale of humans (ie. the flood scene). The directors acknowledge this discrepancy.
Z and Barbatus are standing side by side in formation. The platoon then executes a right face and Barbatus encourages Z to move up putting him side by side with Barbatus again. While this is convenient for conversation, it wouldn't have worked because whomever had been in front of Barbatus in formation would now be in that spot.
In real life, the situation between ants and termites is reversed from their roles in the movie. Ants prey on termites, which are much smaller - and ants are the ones who secrete acid to kill them.
Z would have been in no immediate danger from the water. Ants can survive for days, even weeks, under water.
All the worker and soldier ants in a colony are female.
In real life, female ants make up the vast majority of any given colony.
Cutter is depicted as having wings, as are the large, unidentified flying ants during the ant march to the termite colony. In an actual ant colony, the only winged ants are the princess and one or more rather wasp-like drones. When the time comes to establish a new colony, the princess takes flight accompanied by her flying drones. It would make more sense for Mandible to have wings, given he's the princess' fiance.
When Z drops the wrecking ball, it harmlessly bounces and rolls, having no effect on the same types of materials that it smashed right through a moment earlier.
Z mentions labor and Bala asks about giving birth although ants and other insects do not give birth but instead lay eggs.