After a merge commit, the node in the tree view that indicates the uncommitted changes has parent lines drawn to the merge commit, AND the head of the branch that was merged into the commit prior (see attachment: see that the uncommitted node attaches to the head of the green (leftmost) branch, and the head of the purple (second from left) branch that was merged with the green branch the last commit). After committing, the new commit only has one parent (the merge commit), which is correct. It's only the view when it's not committed yet that's inaccurate; it should only point to the head of the currently-active branch.