We use the Dialpad plugin which works well for the most part. The annoying thing is that if the phone number is in more than once, is not in the exact right format, or they called from a different number, it adds it as a separate entry into Hubspot. I know why and don't expect you to be able to do anything about that. My issue is that I often have to go through and manually change the association of each call on the page. IE if there were 5 calls to/from a user on the wrong hubspot entry, I have to manually click change association, then Contact, then enter the name or email. I then delete that extra contact. It could also be emails, so not limited to just phone calls.
My suggestion would be when you do it for one entry, have an option, like a checkbox, to "Associate all entries to this contact". Alternatively the option to select which entries will be associated with a "checkbox to the left" system.