That was the problem with the show, they should have been in much worse shape by the end of the series than they were. After 7 years, assuming that each season represented a year in their time, with no time in space dock for proper refit and maintenance and not to mention the lack of Starfleet parts there's no way that the Voyager could have been in the shape that it was. Then there's expendables like photon torpedoes, something that the writers seem to forget are actually finite, I imagine that if they gave a count to their photon torpedo compliment once hitting the Delta Quadrant and counting how many they used over the course of the show I'm betting that they used more than they actually had. Of course, they'd probably explain that problem by saying they acquired torpedo housings somewhere, guidance systems elsewhere, propulsion systems yet somewhere else, and they provided the anti-matter themselves.
Then there's the matter of crew, between all of the baddies they encountered over the course of the show, shouldn't they really be down to a skeleton crew? The crew compliment of an Intrepid class ship isn't all that large and they lost quite a few when arriving in the Delta Quadrant, of course, most, if not all, of those losses were replaced by Maquis from Chakotay's ship but they were the last Alpha Quadrant reinforcements they got. They only managed to acquire 3 new crew members from the Delta Quadrant with one of those eventually leaving for a net gain of 2 people. Yet despite all of the battles they got into and the bad things that happened they somehow managed to arrive back home with pretty much a full compliment, how's that possible?
Then there's the matter of their free rides of hundreds or thousands of light years at a time from various sources. I've always wondered if the producers kept track of those numbers along with the progress that Voyager was supposed to have made from episode to episode because, personally, I always thought that Voyager was much closer to home than the writers said it was because I seem to recall them getting a lot of free rides every season that knocked off years from their travel time every time it happened.