When processing event registrations where they have registered on behalf of an organization, you may encounter an issue where a new organization is created and linked to the registration when linking the constituent record to the transaction.
We are currently evaluating this issue and will update this article when we have more information.
As an alternative solution, Please link the organization to the event registration prior to linking the constituent.
Steps to Duplicate
In RE, select the NetCommunity plugin
Select Event registrations
Link a constituent record to the transaction
See that a new organization has been created and linked to the registration