If you take a backup when there are TEMPORARY tables in the database, and you use those temporary tables to update or insert into normal tables, then applying the MySQL binlog to a backup can fail. That is, you may not be able to roll forward the backup using the MySQL binlog. The reason is that TEMPORARY tables are not copied to the backup. And, actually we cannot copy them to the backup, because the names of temporary table files #sql*.frm do not correspond to the logical table names that MySQL writes to the binlog. This problem might be removed in the future, if MySQL implements “row-level binlogging”.

mysqlbackup cannot back up HEAP, or BDB type tables.

Currently, mysqlbackup requires that innodb_data_file_path contains only plain files, not paths. That is, specifications like innodb_data_file_path=/dir1/ibdata1:100M will not work.

Currently, if the regular expression for the --include option does not match any table names, all file-per-table tables are included in the backup.