The theory that the lone fighter took one bomb and detonated it while the Strategos later took another bomb when he left after the battle, leaving the third for us, is likely accurate.
Tactically, whatever they were fighting seems to have seriously outgunned them; none of the initial sally appears to have survived. On the other hand, judging from their deployments and the fact that in the second wave they sent only the one ship, it was probably a *small* attacking force, or it would have likely been too dispersed for the single weapon. Maybe a couple of capital ships like the Bellarion in formation, or something the size of HBX Vircus / Gateway, though such things don't usually move. It would be consistent with trying to attack the Great Omphalos Dust Wyrm, as an example of large single moving target with unknown offensive capability, but there's not hard data either way on what the opposing force consisted of.