I guess you are running MySQL > 5.7.31, just to confirm could you run:
mysql --version
Have you configured tablespaces in your MySQL database?
- Yes → You should add the process privilege, however it’s important to note that there is no tablespaces configured by default in the passbolt database
- No → You could run the mysqldump command with the --no-tablespaces option
mysqldump -u [passbolt_db_user] -p --no-tablespaces [passbolt_db_name] > [output_file.sql]
In the meantime, I’m pretty sure that this blog article will make your life easier 
Finally, even if it displays an error, the file containing the data should still be accessible in the outputed path.