The Second Wave is bugged. If you made it through without a hitch, you should consider buying a lottery ticket because you're lucky.
Doc Lee had to logout and back in to get through it. There are a few minor bugs and two major. The sticky keys during ground combat I consider a major flaw. Doc Lee either couldn't use most of his abilities or they were delayed (as someone said until after death). The second major bug is that when your char warps to Bajor, it resets your mission progress to the start of the Borg Conference discussions.
Link to the official Second Wave bugs thread on the STO forum.
However, Doc Lee made VA in between the failed attempt and redoing the mission. He got his butt kicked in the Nebula Refit so he decided to try out the Odyssey Star Cruiser.
Pros - Gained Engr console slot,gained slot for Cmdr Engr (lost Cmdr Sci slot) extra weapon slots fore and aft, gained device slot
Cons - Lost a Sci console slot, lost slot for Cmdr Sci ( went to Engr), could not transfer Detection console (but didn't need in this situation)
This is not the Odyssey that Doc Lee test drove, Cryptic did a bait and switch. :-/
The loss of the VA ship token is a kick in the teeth. I guess Cryptic thought that the majority of players affected would be eligible for the 600 Veteran's Award. I'm still a couple of months away, so Doc Lee will have to wait for his Intrepid Refit. For now he'll make do with the Odyssey Star Cruiser. At least it plowed through the Dominion ships like a bull in a china shop.