How are the users creating the new/duplicate companies?
When you add a new contact with a known domain name, they should be auto-associated with the existing company, providing the option is enabled on your account.
If they're setting up a new company manually, HubSpot already tries to prevent them from creating duplicates based on domain. Try it yourself - you should see the following:
In other words, you have to explicitly tell HubSpot you want to create a duplicate company with the same URL...
Unless I'm missing something, I'd suggest this is more of a training issue, and users may need to be taught how to use the system correctly.
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