Sorry, I misunderstood what you were saying earlier - that's what I get for trying to think too soon after a weekend! You mean the control ids in the form designer. I've had a lot of those too with no rhyme or reason. I've even had them appear when loading a previously saved project that showed no errors before - meaning it changed the control id of some element either during saving or loading. It's apparently random and fairly easy to fix so I just have it reassign the id and ignore it.
If you're getting them frequently or consistently with one project, you might try opening a ticket and attaching the project so PTS can see it, but I've never been able to get an example that could be duplicated consistently.