Who says they're normal flames? A bunch of the time if you watch ds9 when the klingons attack anything with they're plasma disruptors and hit a target, the start trek FX people were cool enough to do an effect in the tv show where you can watch the plasma dissipate after it hits its target. That's not really fire, but one reason you would be seeing flame like things in space.
Another thing is that terran and vasudan vessels both have atmosphere, if you ever see flame jetting out of a vessel in space after a missile hits or something, it's probably because the missile obviously caught something on fire, breached the hull, and is being fueled by the currently venting atmosphere through the breach.
As long as fire has an oxygen source from say venting atmosphere in a hull breach, sure you'll see fire in space, until all the atmosphere gets vented. Not to mention at which the speed the atmosphere would be venting, you'd have some seriously huge and stoked flames that would be jetting out of the ship in an upward fashion(depends on which direction atmosphere is venting).
Also vessels in fs2 are very big, even the fighters, but i'm talking about besides the fighters, big vessels have lots of atmosphere, so you'd have some fires going on fore some time.
