The ship wasn't shown to have very many clones left aboard when Grievous was on his way to the bridge where he got the self destruct message, other than bodies. There weren't that many bodies all over the place either. Really it looks like the armored troopers retreated and no one told the navy officer clones or whatever they are to abandon ship. They must have made it out via escape pods although we only saw a few. Granted, I would have figured that despite Obi-wan's best efforts the escape was an every man for themselves type thing and casualies were very heavy.