I'm just making the shocking experience that overall difficulty of CZs seem to be dynamically adjusted by the efforts of human opponents - regardless of modes and instances! I have no evidence, but the lucky opportunity to check this mechanic in action. I'm living in a very calm system for many years now and I know how the CZs feel here, including the mild random variations in difficulty. The lucky incident was when a few days ago I met and had a (smack-) talk with some members of a squad who more or less declared war to me. With the result, even though I don't see them anymore in open, the overall difficulty of CZ's has increased significantly!
Exactly the way I would expect and how it should be, as I should have no realistic chance to win against the concerted efforts of a group of players (unless I'm an uber combat ace perhaps, what I'm clearly not). I can't remember the last time where I had to bail out from a CZ due to ammo shortage, too much damage in the early phase or just to prevent losing that battle - and that even 3 times in a row. One CZ I actually lost as it surprisingly turned against me very late in the final phase.
Looks like I'm losing this war, but these dynamic mechanics (if they actually are what I think) are mind blowing!
What has this to do with the OP?
If what I see is true, you have to keep in mind whatever happens in your local instance can be massively influenced by other commanders, regardless of mode or instance. I admit I'm somewhat biased as I always wished FD would introduce such a cross-mode dynamic form of CZs - now I'm almost sure they actually did it!
What the OP describes - if occurs frequently - sounds indeed like a (multi-crew?) bug though. I'm used to some occasional oddities in CZs, even empty CZs from start or suddenly a blob of enemies popping in when I'd already won the war, but that's all a while ago or as an exceptional case at best.