MU Theme conflicts and how to debug theme

Hello everyone!

I'm working with a few beta installations of my current Multi Site project and on a few of them I have some trouble with the whole network. I have a feeling that these errors might be caused by plugins or themes but I can't find them by turning them off.

Is there any way to debug Wordpress Theme & Plugin conflicts.
Can themes that are not used even cause any conflicts?

Thanks in advance for any help!