The core bombers thing is a bug relating to the Devourer golem freeing ships, the upcoming 3.039 will hopefully fix the last two ways that the Devourer could cause this issue.
The wave of 700 ships after 10-15 minutes is quite extreme and unrelated, though. I'm curious if you used some cheats to get some special ships, or how many players are in the game, or if you're using a multi-planet or some AI modifiers that might cause it to be that high. I guess if you're playing against one of the raider-style AIs, it is also feasible that is just that AI type. I highly doubt there is anything wrong with this one, but there are a wide variety of possible causes for it.