So I've noticed that the AI is sometimes able to send a fleet to star controlled by Star Harpies, lose the battle, yet still manage to colonize a planet in the star.

Is there a trick to doing that, is it a bug, or just an AI thing?

OK, I think I might see what it is. If they are able to escape with at least their colony ship still alive, it can still colonize as it still counts as in-system, even if retreating. Sound about right?

The Harpies don't seem to mind the colony though, they don't destroy it and wait for an AI fleet big enough to kill them and secure the colony.

They are just regular Star Harpies, would the larger ones destroy a colony?

Probably a bug - I suspect the "AI colonises planet" event gets resolved before the "Harpies attack AI fleet" event.

Do you happen to have a save where it happened, to make it easier to debug?

The AI's interaction with the Star Harpies is... unusual, so I can imagine cases where a colony ship might be able to slip through.

Harpies don't attack planets, so if a colony is established, they won't bother it.

Well, it seems you can take advantage of the AI with this before they can.

I saw an AI fleet heading to a Harpy controlled star and sent a colony ship to it timed to arrive on the same turn.

When it got there I was able to establish a colony, and then the Harpies and Humans fought it out. The Harpies chased out the Humans and my fleet got there a few turns later to mop up the Harpies.