Xcarve overlapping finished area

I just finished calibrating my machine through machine inspector following the calibration guide below, since I upgraded my belt and my pulley to 9mm. After the calibration I ran a test cut on acrylic and the results were a lot better than before the calibration, but, I can’t seem to figure out why I’m getting this overlapping result?

I’m cutting out a square and towards the right side of that square it’s cutting a line on my finished project.

I also made a video so you guys can see what I mean.

Calibration guide: https://static1.squarespace.com/static/5ae48f2ff8370a31bbd29e9b/t/5b85f4c58985830ad9030c14/1535505629195/Calibration