I had the same just now, and my auto safe was not on.... did you find out what was wrong? all my other projects work except for that one... was using puppet tool and rotation together and all of a sudden this message :/
No, never figured it out, but am almost positive that you just need more RAM, What Adobe doesn't tell you about their wonderful production suite is that it requires an enormous amount of memory and acceleration. I've been using Apple's Motion for most things. Let me know if you find out anything else.
Does your artwork have any thin regions like wire? After using the puppet tool from it's release I have never experienced this till now, I'm trying to manipulate a gaming controller and I think it's having issues with the cable section. Putting a solid behind the artwork in the precomp seems to clear the ram error message.
So try using the puppet tool in a scaled up precomp and then scale it down in your working comp.
I get this error message every time I try pickwhipping a 3D layer's position's dimensions to its own X, Y, and Z properties. It can be any 3D layer including a simple solid, and this happens even after I restart my computer and only have AE running. My system has 8gb of RAM so that shouldn't actually be an issue. My memory settings are at the recommended level.