Leave room to square up the sewn unit
The oversize two-at-a-time method starts with squares a little larger than the final unit needs. After sewing and pressing, you trim the HST square. That gives you room to straighten the edges and place the diagonal seam accurately. The trimming step is part of the method, not spare fabric to keep on the unit.
Finish at three inches, trim to three and a half
For a 3-inch finished HST with ¼-inch seams, the QuiltMargins plan starts with two 4-inch squares. Sew and separate the pair, then press the units. Trim each to 3½ inches square. The unit needs that extra ½ inch so it can finish at 3 inches once the outer seams are sewn.
Keep the diagonal seam aligned
Use the diagonal line on your ruler to check the seam as you square the unit. Check both the size and the seam position; a square can measure correctly while its diagonal is off. Follow the trimming instructions for your ruler, and make sure the corners sit where the next seams will need them.
Test the method on one pair
Make and measure one pair before cutting all the starting squares. A different HST method, seam width or pressing approach can need a different starting size. This calculator's recipe is for oversized two-at-a-time units, so don't mix its starting sizes with a no-trim or multi-at-a-time method.