Mp3tag can work with the tag-types ID3v1, ID3v2, APE in a special but not independent manner.
Please have a look into Mp3tag settings ... "Mp3tag/Tools/Options/Tags/Mpeg".
There are three sections "Read", "Write", "Remove".
Within each section each tag-type can be treated for itself.
Depending on the settings, that means desired by the user, each tag-type can be treated differently.
So it may happen, that the tag ID3v1 and the tag ID3v2 got stored different data.
Or otherwise the tag ID3v1 and the tag ID3v2 may contain the same data in the tag-fields under the same tag-field names, which both tag-types can share, because ID3v1 is a subset of ID3v2.
Within Mp3tag the tag-type APE dominates the ID3 tag-types, other applications behave in other ways.
Once the APE tag-type has been set to be read, Mp3tag does not show values from the ID3 tag-types.
If you want to remove the tag-types ID3v1 or ID3v2 or APE, then activate the fitting checkboxes within the section "Remove".
Leave the dialog with "OK".
Select the tracks.
Apply the Mp3tag menu option "File/Remove tag" or press [Ctrl+R] and the tag-types will be removed at once.
If you need to "undo" the last step of removing tag-types, then keep in mind, that only the tag-data will be restored, which have been set in the checkboxes in the section "Write" within the Mpeg settings dialog.