No, the AI isn't cheating but we understand it can sometimes appear that way. We are always looking for a better way to communicate minion AP generation.
Enemy teams that contain minions generate a couple of AP each turn, for each of the abilities that they have. For example, a H.A.M.M.E.R. Commander will gain the team 1 Yellow AP and 2 Purple AP per turn, while a H.A.M.M.E.R. Soldier will gain 1 Green and 1 Purple AP per turn. This AP is gained at the end of the player's turn.
Also, please note that some characters steal AP. These characters include Black Widow, Yelena Belova, Mystique, The Hood, and Blade.