If I do a pocket cut of a rectangle, the inside corners are not "square" with the radius of the cutting tool. For example, I use 1/4" router bit so the inside corners should have 1/8" radius "fillets". On my "new" CNC router that can do 60 IPS, the inside corners have 1/2" or larger "fillets". How can I fix the problem?

Program a radius in the corners. You can program center line of the cutter or part program.

How can I fix the problem?

In General Config, Check Use CV on angles and set it to 89° or 90°.

The proper fix is to increase acceleration, if your machine is powerful enough.