I just went through the same issue and you need to add it to the "Multi-line" view. For instance we wanted to include a lookup to a partner account when adding the product and we then added "Partner" lookup field to the "Multi-Line" view (it's next to the mini console layout.)
Hope this helps.
Without seeing your org, it is impossible to say for sure, but almost certainly what is happening here is that you have triggers consuming this governor. Most likely would be triggers on OpportunityLineItem itself, but you might also do cross-object logic which then interacts with other triggers and consumes more queries.
The upsert keyword in and of itself ...