When running the diff tool in changelog mode, temporary tables are created as permanent tables in the changelog.
Ideally the diff tool would recognize that they are temporary and create the appropriate tags for their creation, but I would be also happy if their creation would be skipped. The reason is that on a summary inspection of the reverse engineering process they do not stand out and the error is discovered much later.
As a technical solution, if you are using the USER_TABLES dictionary or to retrieve the tables you should check for DURATION IS null to get only the permanent tables. Temporary tables have values of SYS$SESSION or SYS#TRANSACTION.