So I am building a new interior cell, and when I ran what I had in game a Dwemer exit piece and various boulders around it had little patches of shiny blue surfacing on them scattered. It wasn't everywhere, only this space. Is it because of too much item clutter (I used a lot of boulders to close two gaps, and I intend to go clean it up a bit and use less boulders)?

a pic or video of what you're seeing would help... I don't think I've ever seen anything like like you're describing.
Perhaps even upload an esp so we can see if its just you or not.

I would post a link to the picture, but I'm not allowed. I sent one as a PM to you. Hope it helps.

http://www.flickr.com/photos/77257964@N04/6778312492/in/photostream/lightbox/

looks like the effect that's added to Falmer pieces.

Did you use any ceiling tiles from Blackreach?

It looks to me like you have the ceiling tiles too low and are being exposed.

Ah, that could be it. I could have accidentally used the falmer version on those pieces.

Ah yea...I forgot about some of the Falmer pieces.

Ha yep, that was it. Thanks a lot!