So I've lost ships before, and they usually just explode after taking too much damage. But in this one combat vs a space station all my ships suddenly disappeared in purple vortex's.... what was that?

This is in Moo 2 btw.

Purple vortexe is a bit vague. But it sounds like either your ships were hit by a Black Hole generator... or their main reactor was critically hit, and the purple vortex was the resulting shockwave.

How many was "all" of them? A black hole generator can only target one ship at a time and the effect is fairly visible, so unless they were up against another fleet equipped with generators (and I don't think the AI normally does that), it's unlikely to be a BHG attack.

I had 3 ships, and then 2 of them disappeared with that spiraling purple circle. Then the next ai combat my last ship went the same way. This was early game against a weak empire so i don't think they had BHG yet? Actually as i recall the space station was using mainly missiles.

Here is the effect i was talking about, though i did not take a screen shot at the time.
http://www.forceforgood.co.uk/wp-content/uploads/2012/11/moo2_2b.jpg

Its the BHG, right.