Depends how blatant you're being about the dungeon not making sense. If you present a standard orcish lair, but somehow forget the latrines, I'm probably never going to even consider that the dungeon doesn't make sense. By contrast, if you present a standard orcish lair, except that every room turns gravity through 90 degrees, then I'd expect you to explain that at least to the DM.
Assuming we're talking about the latter case, then I expect a dungeon to make sense, except where it makes sense that it doesn't make sense. So, place your dungeon on the Plane of Dreams, and you can do whatever you want - it makes sense that it doesn't make sense. Have the whole thing possessed by the insane remnant of the dead god, and you can do whatever you want - it makes sense that it doesn't make sense.
But present a clearly nonsensical dungeon without such an explanation (presented to the DM - of course, the players may never learn the secret), and I'll reject it. Because not only does it not make sense, but it doesn't make sense that it doesn't make sense.
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If, by contrast, we're dealing with the less blatant non-senses (such as our orcish lair with no latrine), then that's really not all that important. If I spot it, it's a mark against your dungeon, but it's a long long way from being a deal-breaker. Indeed, if the rest of the adventure is a 5-star effort, a mistake of that sort really isn't enough even to drop it to 4-stars. Basically, it's like the occasional typo, grammatical error, or stat block snafu - it would be better if it weren't there, but it happens and I can live with it.
I hope that helps!