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The usual reason for this is the creation of shared cell definitions during the merging process of dxf and dwg files into MicroStation. The shared cell definitions have component elements which occupy levels even though the definition itself does not display. If a shared cell instance of one of these definitions is placed in the design you cannot delete the shared cell definition nor the levels their component elements reside on.
To fix this you will need to drop any placed shared cell instances to either normal cells or components and then using MicroStation compress, delete the unused shared cell definitions and then finally you should be able to delete the unwanted levels.
To start, select all shared cells in your drawing using Select by Attributes and then drop them to either regular cells or component elements using the drop tool. MicroStation tool settings for the drop tool allow you to set whatever way is most appropriate for you.
After the shared cell instances are dropped you will then be able to compress out the unused shared cell definitions. The next step is to then remove all unused shared cell definitions from the design. This can be done by choosing File|Compress|Options from the main MicroStation pull-down menu. Once the "Compress Options" dialog box opens, turn on "Delete Unused Named Shared Cells" and "Delete Unused Anonymous Shared Cells". Now compress the file. Because shared cells can be nested I would recommend running the compress function several times to ensure all shared cell definitions are deleted. Once they are all deleted you should now be able to go into the level table and delete the levels you no longer wish to use. Let me know if this handles the problem for you!