Hello Alex,
From the description and the error message, it seems like a case-specific problem with the MySQL.
I was able to find this
report with a similar error you are encountering. For more information on InnoDB File-Per-Table Tablespaces, you can refer to
this MySQL documentation.
However, this seems like a question that would be better posted to
DBA stackexchange and
MySQL forum where you have access to a larger community of database enthusiasts and experts to share ideas with and get support from. Make sure to include all relevant details and error messages which would help the community troubleshoot.