Hi @Anonymous , @matthew_goulart , @martongr ,
Sorry to hear that you're having trouble.
May I know where the libraries you used to import and original libraries is come from?
If the libraries were downloaded from ultralibrarian.com, there is a known issue that importing the downloaded Fusion360 PCB libraries from there could result the unexpected footprint different version error issue.
If this is the case, please download the Eagle6 Library instead and then create the library in Fusion with the downloaded script by yourself, and later importing library will have no such issue.

If it's not the case, do you mind to attach the 2 libraries which cause the issue that we could have a check?
You could duplicate the libraries and just delete others devices but only left the ones which have the issue in the new libraries.
Thank you very much for your help and so sorry for any inconvienence.
Best regards,
Helen
Helen Chen
Principle QA for AutoCAD Windows