I think there are three categories of problems here:
There's things like the Enterprise E growing by two decks during a movie, the Defiant changing size, the Delta Flyer not fitting inside Voyager, Book's ship clipping Discovery's landing bay etc. Things that most people aren't going to notice, and would often need to examine screencaps to prove. Mistakes are going to be made and sometimes the artists will bend reality slightly for a better shot, it's fine.
Then there's things like Discovery's turbolift dimension, which is the producers blatantly going for spectacle over reality and assuming no one will notice or care. The trouble is that it's so obvious that the moment you see it, it breaks the spell of the episode. It can't be real, so I don't take it as real anymore. This is not good.
Finally there's things like Voyager's torpedo count and infinite shuttles. Personally I didn't keep count of Voyager's torpedoes and I doubt many people did, and you could easily come up with explanations for how they got more. The trouble with Voyager's resource issues is that they were set up to be a big part of the series and something we should care about, so it's less that the writers were abandoning reality and more that they were abandoning their premise. Which is arguably worse.
I guess what I'm saying here is that different people will be able to overlook different things, so to say that story and set pieces matter more than consistency isn't always true. It certainly isn't true for me, because a flashy set piece is just noise on the screen if I don't buy what's happening.
