Are you importing afresh from the in-game add-on and is the version you’re using up to date?
You also may need to open all your characters’ bank tabs to make sure that what’s being shown as upgrades isn’t still in your bank.
For peace of mind:
Open all your bags, incl. bank ones.
Access all your characters’ spec.'s that you use.
Also, while you’re on the AMR page for the character concerned, do a Ctrl+F5 to hard clear the cache that’s held for them.
Once that’s done - bear with me - delete all gear sets in the character tab (in game) & re-export the data-string to here & re-run BiB… then run Upgrade finder.
If that’s still the same, at the top of the BiB or Upgrade finder, you’ll see a Help button… use that to generate a character snapshot that can be published/posted in a reply so that others can use it to get exactly what you see so that they can try to replicate what you see to help ‘debug’/assist you better.