Os arquivos de tabela que você está vendo provavelmente são resultantes de uma operação ALTER TABLE que não pôde ser concluída. A parte relevante dos documentos do MySQL diz:
If MySQL crashes in the middle of an ALTER TABLE operation, you may end up with an orphaned temporary table inside the InnoDB tablespace. Using the Table Monitor, you can see listed a table with a name that begins with #sql-. You can perform SQL statements on tables whose name contains the character “#” if you enclose the name within backticks. Thus, you can drop such an orphaned table like any other orphaned table using the method described earlier. To copy or rename a file in the Unix shell, you need to put the file name in double quotation marks if the file name contains “#”.
então eu simplesmente emiti um DROP TABLE
neles. Nota: Não simplesmente exclua os arquivos - caso contrário, você obterá as chamadas tabelas órfãs produzindo avisos de mecanismo de banco de dados como estes:
InnoDB: in InnoDB data dictionary has tablespace id N,
InnoDB: but tablespace with that id or name does not exist. Have
InnoDB: you deleted or moved .ibd files?
InnoDB: This may also be a table created with CREATE TEMPORARY TABLE
InnoDB: whose .ibd and .frm files MySQL automatically removed, but the
InnoDB: table still exists in the InnoDB internal data dictionary.