I created a new, stock Gold game and edited the Alien Traders to have a level 2 homeworld and 15 aliens on day 0. Then I rebanged the game, edited my ship, and invaded their planet.

I've done this twice and noted a few strange things both times.

Several times I found myself dropped from the planet or citadel prompt back to the command prompt without any message about being evicted. For example, I'd press enter at the citadel prompt and find myself at the command prompt, no messages in between. (I did see the eviction message at other times when I let the aliens invade and reclaim the planet.)

Sometimes, for several seconds after landing, aliens continue to attack me ship-to-ship.

And while on the planet, I get messages about aliens warping in and out of the sector. Is that normal?

I'll recreate your test conditions and see what I can see here. I'll let you know what I find out.