That been like for a while now whether this is a bug or deliberate I don't know for sure.
When I can't get NR for more or less constant invasions, and I'm in NS, I tend to go through side and head straight through oil and warehouse up and over silos, and down other side, then continue with rest, that way if invasion starts while doing front of fact I can finish cog set and still have time to do centre silo before it finishes.
Everytime I pass through warehouse a second time there are two more goons running around, and i'm sure once I defeated those two and when I entered a third time ther was at least one more again. And yes one of my toons could sometimes not see them too.
I would say this scenario extra goons and invisible aswell is probably a bug, as normally you wouldn't go back on warehouse, other then for reasons you stated or I just mentioned above, so what would be point of adding more once passed warehouse.
I can also confirm they do damage wether your toon sees them or not.
'Keep it Kool

'