I had the same problem in the Solomon Island area, where around 20-25 B-24, B-25, HudsonIII(LR) and B-17 groups sometimes just didn't fly for days on end. I couldn't figure out why.
However after slowing down the replay, I managed to nail one of these instances where 20+ groups didn't fly to just one quick message that appeared on screen, during the PM phase of the replay, see the picture.
This message just displays once on screen during the replay, no matter if you fly 1 BG to the target or 250.
It cannot be found later in any of the reports as far as I can tell and doesn't appear in the log in the lower left corner during the replay, so it is very easy to miss.
Like rustysi points out, you didn't provide a lot of information, so I might be wrong, but studying the on screen replay carefully could clear things up.