Star Trek: 11-ish Times Voyager Lost A Shuttle
5. Class 2/Type 9, Name Unknown/"Federation Starfleet" — Dark Frontier
Voyager had so many shuttles, it seems, or, at least, the ability to build more, that they could afford to use and lose one as Borg bait. That said, remotely piloting a shuttle with three false bio-signatures was quite a clever ruse to get a Borg sphere to lower its shields, even if the Queen was spying in on 'Operation Fort Knox' the whole time.
Interestingly enough, all we see of the Class 2 in Dark Frontier is from the Borg's perspective. We don't know what the shuttle's official name was, but the Borg, as is their more utilitarian wont, call it "Federation Starfleet. Class 2 shuttlecraft." We can safely assume it was right royally assimilated.
The partial assimilation and crash of another ship that featured heavily in Dark Frontier — the Hansens' USS Raven (in 2350) — had already indirectly caused the potential loss of another Voyager shuttle in season four. Keep your homing beacons on for more on that later.