This is most surely a glitch, though when I was meandering through Stony Creek Cave, I came across this hole leading in to a tunnel that I just couldn't reach without Whirlwind Sprint. So upon using it to reach the tunnel, it took ms to this place called Kazengrel(sp?) where a strange orb appeared with about three dead bandits surrounding it. I touched the orb and a cage trapped me before the orb hovered around the room. A moment later, the floor opened up beneath me and I ended up falling for hundreds of feet then landed in an ubderground lake. Followed the tunnel leading out of the lake and ended up in Stony Creek Cave or whatever. Weird.

Im failing to see the glitch...

I ended up in the beginning of a Dwarven Ruin when I should have ended up at the end of the dungeon.

Glitch.

Should have made that clearer, I apologize.

That's supposed to happen.

I found this on the UESP wiki:

Kagrenzel is also reachable when entering from Stony Creek Cave. When you reach the end of Stony Creek Cave (the area with the waterfall and moonstone ore) you can use your Whirlwind Sprint shout from a nearby rock to get on top of the waterfall. This is a faster way to reach Kagrenzel, but you'll miss out on a thrilling plummet. Note that the area with the glowing orb is not reachable if you enter from this way. Unless by an underwater texture glitch, as demonstrated in this video: http://www.youtube.com/watch?v=DhqbhEtNzH0

Maybe this is your problem?

Weird, I started at the beginning of the dungeon, not the end of it, despite reaching it by taking te route that should take you to the end. So yeah... That's the glitch.