Are you using steam when pressing the blocks? It can cause shrinkage.
Check the individual square sizes. The outside ones should be 3 1/4 to account for seam allowance when sewn to the next block.
The inside squares should be measuring at 3 inches each finished.
Have you checked the pattern for corrections? There may have been corrections posted.
How are you making the HST? Is it 2 squares of fabric placed right sides together, sewn and cut? What size square are you starting with for the units?