I haven't really played NeoLemmix until the recent level solving contest, and multiple times I thought I hit some weird bug where the mouse stops detecting lemmings. Eventually (as in sometime today), it finally dawned on me that I might have had directional select on, and forgot about it after multiple rewinds and trying different things etc. The mouse cursor looked like it's not detecting the lemming and it seemed like assignments to the lemming didn't work, when in fact it was just that the lemming was in the wrong direction from the forgotten directional mode.
Now that I know what to look for I won't be confused again, but before that when I didn't know what was happening, I wound up restarting the game, which is a little annoying. If the mouse cursor looks a little different during directional mode (eg. have an arrow at the left/right over the usual crosshair), this confusion would not have occurred.