What type of assets are they? (images, scripts, css, other?)
If the Advanced Export cannot make an an appropriate determination on if an asset should be used or not then it will require the asset (checked and greyed out). There's definitely a case that it should be checked but enabled so it can be unchecked, which is a long standing feature request.
Of course, if you're absolutely certain it is not used, then you can manually delete it from the export after-the-fact.