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Dear Seth Pullishy,
Good day! Thank you for posting your query in our community.
Based on your description, you encountered a problem when making a group access only one library.
Generally, you can assign unique permission for these two libraries via Settings > Library settings > More library settings > under "Permissions and Management" section > select "Permissions for this document library" > if this Library is inheriting the permission of the site, then you need to Stop Inheriting Permissions first to grant the unique permissions for this Library > then delete Site Visitors and Site Members group (do not delete the Site Owner group and make sure the admin or owner in this group) > then you can grant permission to a group. Repeat these steps on another library.
May I know what problem you have encountered? You can provide more details like screenshots for us.
Sincerely,
Jazlyn | Microsoft Community Moderator