A DGN file contains a lot of empty levels that can not be deleted. Compression and cleaning does not help.
The following wikis describe how to query / view the usage of the layers and delete them:
How to Query Usage of All Levels
In the example case, the affected layers are used in models "EXTRACTION_USTN54795" and / or "EXTRACTION_USTN78476".When you set your reference presentation to "True Hidden Line", MicroStation creates a new model in your master file. The model is created such that it doesn't show up in the Models dialog to avoid confusing people. The model is generated by the hidden line processing, and contains a hidden line "snapshot" of what's in the reference (and its child references, if nesting is turned on). If you change some geometry, you must do a "reference reload" on the reference to regenerate the hidden line. We decided not to make the reload automatic as it can be quite time consuming.
If you want to see the models that we create (and be able to go into them to edit them - they are ordinary models for most purposes) create the new configuration variable MS_INCLUDEHIDDENMODELS and set it to any value (the value ist irrelevant, only the existance of the vairiable counts). If you edit the generated models, keep in mind that doing a reference reload on that reference file will overwrite all your changes to it, as will changing the reference presentation to something else and then back to True Hidden Line.