If you are starting with 3" squares, the block should equal 8" (3" x 3 = 9". Subtract 1/4" x 4 for the four pieces in the two seam allowances. 9" - 1" = 8").
Measure the center square of your nine patch - is it exactly 2-1/2"? If not, your seam might be off a bit. Not all 1/4" feet are the same, you need to test it to be sure you're lining up properly. Or you may need to move your needle position a bit.