Short answer
HubSpot's KB: manual creation warns if the domain matches an existing company's primary domain; imports deduplicate on primary and secondary domains unless you choose a custom unique property. Companies created through the API, including sync apps, are not deduplicated by domain. If several companies share a domain, automatic association links contacts to only one of them, and you can't choose which.
1. Find them
My demo portal shows 85 company duplicate issues.
2. Real duplicates vs branches
- Same business entered twice: merge.
- Separate locations or subsidiaries: use parent and child companies.
3. Related
Duplicate companies from connector IDs and auto association by domain.