We have the same issue, there is actually another post out there concerning this. I believe there are several people that have shown a need to be able to seperate the info for multiple deals with the same contact. Hopefully HubSpot will be able to make this happen. Below I tried to copy the link to the other post. Make sure to show your support so HubSpot knows this is a needed feature.
I'm just looking at HubSpot and the fact that you can't log emails to multiple deals for 1 customer is a real drawback. All the emails to the client currently go into ALL deals which makes the feature useless and confusing.
Yes it is confusing. In one of the previous posts there is a link to another discussion on this topic. Please make sure to show your support for a fix so HubSpot knows we need a solution for this.