I'll bet that those squares are used to make HSTs. The official way to do these is to add 7/8" to the finished size and cut 2 squares. You draw a diagonal line corner to corner, sew on either side, cut on the line and you have perfectly sized HST. If you sewed the seam perfectly. And you pressed perfectly. And you cut perfectly.
Read the entire pattern and if they are for HST, just round up to the even inch, make your patches then trim down.