It's doesn't seem like something I can do but the enemy keeps disappearing to nowhere whenever I catch up with them and try to attack them. what is this? it's getting a bit frustrating
They can retreat after 30 days in combat.
If you've got all short-range weapons (strike craft included), then several days of 'combat' can pass before you have the chance to do damage, and they can go emergency FTL.
Were they fighting a starbase or outpost?
If AI fleet has been attacking your starbase/outpost and you send reinforcements it is likely that 30 days has passed since the AI fleet begun combat so soon as AI sees your reinforcements arrive it can emergency FTL out. I haven't seen AI to withdrawn immediately in other cases