This is something that's been going on with our server for a couple of weeks now. Everybody's home bases are littered with dead ships that get killed but never vanish. As you're travelling through space you'll find ships that were destroyed by someone just floating in the middle of nowhere; perhaps battles between the trading guild and pirates? They no longer have a faction. The only way to get rid of them is to either salvage them or hit their core to speed up the countdown until it vanishes. Basically, if you don't kill them manually, they never go away.