Yes, it's inconsistent. No, unfortunately, I don't have suggestions for a fix.
My maternal grandparents were 3rd cousins. In addition to being, obviously, spouses, they had multiple in-law relationships. Sometimes FTM shows 6 connections, sometimes 9, sometimes fewer than either. All this without my having made ANY changes on the relevant family branches.
On a good/bad day, depending on your point of view, my GF and I are related 6 different ways.