I ran into this issue myself. I have a process that requires 1 to 12 departments simultaneously to approve an invoice.

The process goes from Form A (invoice insert) to assigning departments to approve the invoice (Form B) to Form C which is the approval form. The number of departments is determined by what the user inputs into Form B. Now I have all 12 department paths available but only the required ones would be active. An inclusive gateway is used to split the paths to each department. Each department task is then attached to an individual Exclusive gateway to determine whether their choice was to send back for review (cancels all other tasks), sends to reject (also cancels others), escalate to higher Approver (loop to same task but with new user assigned), and finally to another inclusive gateway to merge all the departments back if they all approved the invoice.

This is where the problem starts. When 2 or more departments are required and they all approved the invoice, they reach the merge inclusive gateway but then 2 or more out flows occur and go to the approval end. This is quite frustrating because I have redesigned this approval process multiple times. I changed all the exclusive gateways branched off of each department path to an inclusive gateway but this made no improvements. When I found was if I had the department task flow directly to the merge inclusive gateway, the gateway would wait for each active path, then only out flow 1 instance. 

So, what I found out is you have to have the split tasks directly connected to the merging inclusive gateway for the merge to work 100%. Once you have a branched active path hit another gateway, it seems to cause the merge to duplicate the outputs per active path/gateway hit.