Can someone tell me why this happens?

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.

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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.

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How does it render in software when creating the tool paths

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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.

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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.