^That's another problem the seemingly endless supply of shuttlecraft. TNG/DSN could get away with it, they just got a new one from one of the shipyards. But begins to stretch the suspension of disbelief to breaking point.
We are told point blank how many they have and that they can't replace them. It's not my fault as a viewer if I call them on it. All it would have taken is a line drop in an episode saying that they were able to procure some alien torpedeos and retrofitted them.
To create hull plates, one would suspect you would need an Industrial replicator of some type, DSN sort of gives the impression that these weren't as widespread as your ordinary food type replicators. It would make sense that an instalation as important as DSN which served as a repair station would have one. What amounts to light cruiser (Voyager) would seem likely not to have one. But once again they could have addresed that with a line, i.e. "Fortunantly we were transporting an industrial replicator.
I'm sure another inconsistancy is the holodeck power being incompatable with the rest of the ship (from a design view) that makes no sense. I supsect the real reason was related to the TNG ep "Booby Trap" they knew fans would no doubt call them an the holodeck 'wasting' power so they hoped to get around it by making it incompatable. Have they not heard of power converators in the 24th century. I after all charge my DC powered phone from my AC mains socket.