As I've played through Skyrim, I've bounced back and forth between exploring, and doing side quests, and doing the main quest. Early in the game, while exploring, I happened into the Kilkreath ruins and solved the first puzzle in there. Later, a mission is given where you have to take an NPC into the ruins. Because I've solved the puzzles already, the npcs just stop and stare at the puzzle items, waiting for me to solve them.

I am unable to progress in the quest because of this. Any ideas on how to bypass this?

I did the same thing with a cave/dungeon thing..i cleared it before it came to the actual quest requiring me to.

I just went back to it and found i had to do it all over again..

have you tried going back ..it might have reset itself like my cave did.

I went back a couple times. It hasn't reset.

Try passing by time by sleeping/resting... a dungeon that I've half-cleared somehow resetted and all the badies and treasures pop back up when I came back to it in about a week or two after I left it

All of the dungeons reset after 30 days of in game time I think. They reset after a certain amount of time, I took an educated guess on the 30 days part because that's how long I think it took mine to reset.

There's also a mod that you can get that will change the reset times to 1, 3, or 5 or so days if you wanted it.