Disk Space Monitor:
I'm assuming you are seeing this in the admin CP under active monitor. Click on the "active monitor" button (next to the yellow light. Click on "disk". Click on "virtual sites". There you will see a list of the domains, and will be able to identify the site that is over the limit.
Really it is just a warning that the site, or a user in that site, is using more disk space than you have assigned for it. Nothing more. I have one that was assigned 1MB (not by me, but by another user), and they are at 1.2MB so it flashes red.
If you up the assigned space for that site/user the yellow light will go away (once you make changes it will revert back to green eventually, NOT instantly).