I've been sewing a long time. Corners don't always match up. Usually, mine are because some of squares or HST's are slightly smaller than others. I realized that I didn't always have my rulers in exactly the same place when I cut every time. Also, if you are using two different rulers, some times that is a small difference in the measurement. What to do now? You can ease in 1/8". I know that the better way to ease in is to have the oversized piece on the bottom and let the machine help. I don't trust this method. I would rather have the bit extra on the top so I can see if I am going to sew in a pleat or pucker. This is a good video that may help you.
https://www.youtube.com/watch?v=Eh7_zvHcIio
Edited to add: if you sew over the pins, sew very slowly. Hitting a pin at speed can cause your needle to break and you never know where the point is going to go.