This is probably a bug with heat shield. The info on the part says its mass is 0.3, bug when I place it it doesn't affect center of mass indicator at all. Yes, my ship isn't that heavy, placing small girder that is just 0.125 on the same spot shifts the indicator a bit. Testing whether it really is treated as 0 weight by physics is tricky for me, but it certainly seemed like the center of mass was where it was shown in the editor - just above geometry center which caused the ship to flip during descent back to Kerbin despite my attempts to hold it retrograde. There are no fuel tanks on that stage either.