I've noticed a discrepancy between a planets PQ and the actual number of buildable tiles when playing neutral. I've never seen this on planets that I've colonized myself, only on planets that I've conquered. Typically, I seem to be about 25% short (PQ12 has only 9 tiles, PQ16 has 12) but this isn't a hard and fast ratio. At first I thought that perhaps when you conquered a planet you didn't get the PQ benefit of a colonization event that may have occurred, but I notice this on (I'm guessing) about half of my conquered planets. This seems far too high to be caused by PQ colonization events.
I've only played 5 games so far (all on v1.2) and on one of them I was evil (didn't see this effect then) so my sample size is rather small.
Has anyone else seen this?