Apologies for the messy .capx, but this is the first time I've managed to reproduce this reliably (.capx link sent via PM). The problem seems to be localized in two events - 122 and 137.
Event 122 should select the instances of enemybase where enemybase.hittimer is less or equal 0. This appears to not always be the case.
Run the .cap, hold the left mouse button in the direction you want to move. When you're close to the enemybase black oval, it'll move towards the hero. At that point - and only when the enemybase is moving towards the hero (otherwise the bug won't show) and the detector sprite overlaps it, click in the direction of the enemybase to attack it. Doing do will result in the enemybase.hittimer value getting stuck above 0, and the enemybase isn't hit backwards properly.
Next, enable condition 3, "enemybase.hittimer is less or equal 0" in event 137. Run it again, and it works properly.
It shouldn't make a difference if that condition is enabled or not, as that condition has already been checked in event 122.