I seem to recall they're probably Underbase casualties.
Though there is a bit of wriggle room depending on how you define the word (though not much, surely he woudn't leave the unrepairable behind?) the end of Dark Star
has Scorponok saying he's going to collect his "casualties" seemingly with Prime's blessing (and of course, he's not really got the resources to stop him). So we're in a strange world where the book is both being very precise about some minor inconsequential plot points but cheerfully ignoring others as it sees fit.
Thinking about it, a whole load of Decepticons being aboard the Ark in stasis really makes no sense, because either Megatron would have been put in with them post monster-Ratchet and wouldn't have been exposed to Nucleon, or their bodies were all mixed in with the Autobots rather than being kept separately. And Grimlock not knowing about them as he's cheerfully pumping Nucleon into the system is a bit much (and whilst he might have worked around them, that's at odds with his "No need for checks, they're all Autobots!" attitude).
What is odd though is it was also established that there were still fallen Autobots aboard when Shockwave stole the Ark, wouldn't that make for a more interesting zombie army to set against their former comrades?