So, I barely beat a dungeon (like by 0.5 seconds), and it was part of the Shadows in the Desert quest. I turned on my catch filters and as I beat the admin, my catch filters automatically tried to catch a shadow metagross at the end and I caught it. The thing is it didn't count towards my quest (step 26 of shadows in the desert), and it said I didn't finish it in time. I'm not sure if this is a bug though.
#Dungeon not completed in time even though I did
ionic glacier
narrow harbor
it is very likely the catch animation didnt complete before the dungeon timer ran out and that was what caused you to not finish the dungeon in time
stoic badger
That would normally still allow you to complete the dungeon, but in this case, I think because it was a trainer battle, the trainer wasn't considered "defeated" until the animation finished
narrow harbor
though this would probably be considered a bug and would probably just need the same fix that wild pokemon had