Yes, but virtually is the significant word in your sentence. It's misleading to say that CC doesn't have anything to do with it if you do have some in your game. In order to cause a blue lot (or a cutout), you have to place that specific download on your lot, save and exit, then reenter the lot. A lot of people don't make the connection because it doesn't show up immediately. You don't need to have a huge mods folder, all you need is one "bad" download.
When my Sims family went to France and returned for me to find all their (and 3 other families) skills, plants and inventories los,t I had no downloads whatsoever. I subsequently downloaded the updated AM, Supercomputer and bluegenjutsu's Gain Instant Skillwhidden Toddlers - Elder. Nothing else.
I honestly think that it has nothing to do with cc's. I installed WA and sent a family in Riverview to France. When they got back I found that all 4 of my families that I had created in Riverview had lost all fruit, vegetables and fish from their inventories, all skills and all harvestable plants. I spent some time retrieving their skills so their jobs wouldn't suffer and next day went back to find out that every lot except for two on the neighbourhood were blue and couldn't gain access to them. I had approximately six cc files including the updated Awsome mod and the super computer at the time. ( I had taken everything out to install the patch and ep and then put in those I knew were safe)
I have since gone to Sunset Valley and played some families there. I have not sent them away anywhere and everything seems to be fine. Fron this, I think it definitely is a glitch with the ep. I don't think I'll be buying any other new ep until it has been around for at least 3 months, if then.