Why does the laser randomly miss during the cutting process?

This is usually caused by the wood. Plywood is glued from different sheets of wood and the glue is usually not evenly distributed at cheap pieces. I guess you have glue traces inside which aren’t cut through. You can add a few passes to be sure, but depending on the materials they used, you will never cut through at these spots.

I have another theory…

Material doesn’t change so much that it goes from burnt to nothing, there is not even a mark at these random locations. This indicates to me it isn’t lasing.

I think you have an intermittent broken or loose wire/connector. Most likely in one of the moving parts, such as in the drag chain or a connector… I’d bet on the drag chain as this is the where most of the movement occurs.