Well, if you really want to be sinister, as has been said ships should be fantasticly easy to hide; how could pirates hope to find them? By being given a hint, maybe?
Yes, Wolfnet was the best, but ROM was the second best. When the Dragoons began getting ready to recover the ships, it made noise in the Dragoons. Not much, since it was kept quite even internaly, but perhaps just bairly enough to tip off a well placed mole. Amazing coincidance that the pirates and Dragoons arived at exactly the same moment? Or a simple matter of the pirates only learning of the location just as the Dragoons were setting out?
If the WoB (or potentaly even real ComStar, though that's rather less likely) were snooping, they might only be able to learn the location as the Dragoon's own expidition was setting out (at which time many more people are given access to the information). They rushed some 'pirates' out there to see if they could either preempt the Dragoons or else hold them up and cause them problems, the WoB not having any ships of its own at the time after all. But, the Dragoons moved too fast, and caught the WoB's pirates in the act.
If the Dragoons had left some security behind (not people nessissarily, but just simple things like locks on the doors) and it was defeated, perhaps its because the 'pirates' were aided by someone who understood how to defeat such things (or had some extra guns/dropships floating around).
Now, there's not even the slightest bit of evidance for this. But, its a fun idea, perhaps.