In the License Workbench, when you filter the Publisher to a specific one. E.g "Microsoft", then you see 2 "Microsoft" publisher cards.
Check the "Software Subscriptions" list and check the Publisher mapped to the Microsoft-related records.
Notice the "Publisher" is mapped to the incorrect core_company record.
The reason of these data could be that at one time, Microsoft in samp_sw_publisher table is mapped to the incorrect Microsoft ("sys_id") in core_company table, and later was changed to the correct Microsoft ("sys_id") core company.
1. Run the fix script below and replace the "incorrect publisher sys_id" and "correct publisher sys_id" with the related sys_id.
var gr = new GlideMultipleUpdate('samp_sw_subscription');
gr.addQuery('publisher', 'incorrect publisher sys_id');
gr.setValue('publisher', 'correct publisher sys_id');
2. Run the reconciliation again.
Please back up the list of "Software Subscriptions" that is mapped to the incorrect publisher sys id.
Always test this first in a non-production instance before applying it to the Production instance.