Not sure if this is a bug or an intended additional challenge, but I noticed in the lategame (post-bots obv) that the entity ghosts not always stay behind after the biters destroy something, so the bots won't replace the missing pipe/inserter/turret/belt/etc. this causes the oil/ammo supply to break, and especially for the oil it's hard to detect which pipe went missing.

I'm not sure which faction is causing it, it might have to do with some acid pools not allowing the player to build on top of it for a few seconds. I didn't see it happen yet in realtime, but given the frequency at which this happens (like up to 10 times per hour), another guess is that the initial destruction perhaps places the ghost, but then the "unbuildable upon acid pool" happens shortly after, deleting the ghost? Maybe nuclear biters have something to do with it as well? Any type of attack that changes the ground/obstructs building? I know this is all quite vague, but with better coding knowledge than me you might know what causes it better then me. If this is established to be a bug, not a feature, then I can perhaps try to catch it happening on video or such. Anyway, thanks, I'm having a lot of fun with the mod :)

I have faced the same problem, and I think I have an idea of what's causing it.

It seems that sometimes, when biters have a small breakthrough, they'll place these energy sucking crystals. That's not too bad by itself, but when they place them, it replaces the ghost that was there, and when your defenses manage to destroy it, the ghosts would not be replaced. A jank solution that seems to work for me is using the recursive blueprints mod to automatically replace the perimeter every couple of minutes.

As far as I know, this is a Factorio mechanic. If an object appears in the ghost's place that interferes with construction, the ghost's lifespan is reduced to a few minutes or less. This object is acid pools and Energy Biter pylons.
However, in the upcoming update, the pools will no longer block construction. But the update won't be coming anytime soon—there are too many things that need to be fixed (for example, the developers broke the expansion of Biters from mods if their nests can't be placed automatically during chunk generation. This means that "survival mode" is currently broken, and only sieges are works as it should. Fortunately, sieges and resource settlement are working, as if settlers disband, direct generation of biter nests is triggered. So, although Rampant is significantly weakened, it still fights for territory.)...