With the latest docker you can disable the gRPC Fuse for file sharing. (the gRPC Fuse setting is causing this problem, it's incompatible with the data dictionary of 0)
This fixes the problem... You can stop here if you're happy, but to use the new filesystem you can:
- Disable this checkbox
- Start the container
- Dump the database
- Enable this checkbox
- Make sure your data folder empty (so mysql creates a new data dictionary)
- Import the dumped database
UPDATE
Since version 2.5, the setting has been moved to the 'experimental features' page: