This may be caused by the fact that your archaeological work progressed too fast before the science ship arrived or the scientist died unexpectedly in the event for some reason. You can select the planet and use the console command "effect archaeo_site = { set_site_progresses_locked = no }" to solve this problem.

I always thought that it was intended to spawn the drones, to stop progress till you dealt with them. they're a bit OP, i agree, but manageable at end game.
Any idea how much fleet power is advisable against them?