I haven't really had problems with picking or handling multiple enemies independently. An example capx would be easier, but the second half under the "wait" could be organized better (and may be why you're having problems). Give your enemies a private variable 'timer'.
(assuming it's all under a For Each loop)
If state = "wait"
---Trigger once ----> Set speed 0, set timer to enemies.turnTime
---If enemies.timer>0 ----> subtract dt from self.timer
---Else, if enemies.timer <or= to 0 ----> (put your flipping and state change code here as subevents)
A timer, I've found, is a much more controlled way to handle things like this and could be where your picking errors are cropping up.