When ran over a mariadb server running from files copied from a previous versino of MySQL, mariadb first list the tables to repair, that works.
Then it tries to repair them, but looks for all tables in the last database it saw.

[root@hp-dl80gen9-01 ~]# mysql_upgrade
This installation of MySQL is already upgraded to 5.5.47-MariaDB, use --force if you still need to run mysql_upgrade
[root@hp-dl80gen9-01 ~]# mysql_upgrade --force
Phase 1/4: Fixing views
Phase 2/4: Fixing table and database names
Phase 3/4: Checking and upgrading tables
Processing databases
information_schema
a
a.x Needs upgrade
a.y Needs upgrade
b
b.z Needs upgrade
mysql
mysql.columns_priv OK
mysql.db OK
mysql.event OK
mysql.func OK
mysql.help_category OK
mysql.help_keyword OK
mysql.help_relation OK
mysql.help_topic OK
mysql.host OK
mysql.ndb_binlog_index OK
mysql.plugin OK
mysql.proc OK
mysql.procs_priv OK
mysql.proxies_priv OK
mysql.servers OK
mysql.tables_priv OK
mysql.time_zone OK
mysql.time_zone_leap_second OK
mysql.time_zone_name OK
mysql.time_zone_transition OK
mysql.time_zone_transition_type OK
mysql.user OK
performance_schema
test

Repairing tables
test.x
Error : Table 'test.x' doesn't exist
status : Operation failed
test.y
Error : Table 'test.y' doesn't exist
status : Operation failed
test.z
Error : Table 'test.z' doesn't exist
status : Operation failed
Phase 4/4: Running 'mysql_fix_privilege_tables'
OK