How much difference are you seeing?
Are you seeing the difference at the 12/6 position and/or the 3/9 position?
If it is only at the 12/6 position, this is a sign of wear and is not uncommon (although it is typically found more towards the bottom of the cylinder). You should bore and hone the cylinder straight.
If it as present at 12,3,6,and 9 o'clock, not only would I rebore, but I would look for a different machinist.