Hmmm... where to begin.... I suppose I'll just list out a few "issues".
1. It was stated that "Faction ships will never be in lockboxes", yet here are Federation and Klingon ships in lockboxes. Sure they're from the future, but they're still specific to a faction. We know from "Relativity" that the Federation will have the Wells-class timeship in the (possible) 29th century, which means that it is a Federation ship.
2. Temporal ships shouldn't be in our timeline at all. In all cases of interaction with the future, the temporal agents involved recovered their technology almost immediately. Since they can go to any point in the timeline, there's no logical reason that we (or the Tholians) would have possession of them for more than a few minutes, much less permanently.
And for those who would respond with "maybe they're busy with other stuff", see what I typed above. It doesn't matter when they come back to fix it, because they can come back to any point they want.
3. Even if you ignore the above... why are you putting a 31st century uniform (which looks like someone was almost giftwrapped) into a 29th century ship? Where are the 29th century uniforms that actually go with the ship? They look a lot better, and they make a lot more sense for the time period.