Most of the cut was just fine, so I am not sure why this happened (circled in red on the picture). Any thoughts?
It could be a couple of things. If there was a tool change then the zero might be off or the bit slipped from being too loose or from dust in the collet.
We don’t know what the original design looks like so we don’t necessarily know what we are looking at. But, if I had to guess I would say the workpiece or bit slipped or there wasn’t enough precision with the bit, ie it was too big.
How does it render in software when creating the tool paths
I agree, it looks like either you changed tools and didn’t reset your Z axis or your bit came loose in the collet and slipped down. Check for dust in the collet.
I’m thinking that it must be dust in the collet, because I did not change tools. The change in depth came toward the beginning of a cut with a 1/16 bit, then after the first few minutes the depth remained consistent.
In that picture everything should have been cut to the same depth, like in the parts of the board that I did not circle.