I have this happen to me sometimes. My movement keys are different for the main (WASD) and minions (NUMPAD 8456). But my spread-out key (R) can still cause this to happen, where one or more minions will just keep running. When I see this, I just press R again quickly and it's fixed every time. So it looks very much like it's just missing the key-up event the first time.

In your case, if you have multiple keys, you may have to think carefully about which one applied to the minion that's running away at the moment, and make sure to press that key again.