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It is incredibly difficult to debug these things.
I've done it in the past and ended up using a scope to monitor the MD interface and the data interface.
Writing utilities to read and write all the PHY registers under direct human control for debugging.
Many of these PHY chips are very complicated and you will need the full data sheet and user manuals.
The part you are using comes from Microchip so there should be some documentation.
I've used a similar part, also from Microchip (who acquired it when they bought Micrel - KSZ8863)
If you are really stuck it's worth asking Microchip for help.