Hi @LAryan,
Importing multiple objects at once means that HubSpot will automatically establish associations between the records. If you import separate files, HubSpot will not necessarily do that, especially outside of the contact/company relationship. In other words, a deal record might be created from a single object import but the right sidebar of the deal record would not show which companies and contacts the deal is associated to.
If you haven’t yet, I’d recommend reviewing this page: Format import files
It’s crucial to understand how HubSpot deduplicates and associates record before running larger imports.
Let me know if you have any follow-up questions!