I\'ve found a discrepancy between the GitHub network graph and the git log.
Compare the network graph of my GitHub repository called niagara
This occurred for me. Previously the horizontal line in blue on the image below was exhibiting this behavior (like the green quirk in the question). However, doing the back merge (purple line into black, then re-merge into develop) caused the blue line to appear correctly (maybe has something to do with having the same start point as the black line).
EDIT: After further testing and seeing this bug many times in practice, I've noticed that new commits (esp. merge commits that cause the graph to be re-drawn in a new configuration) will often clear the issue and draw the errant branch correctly, with the correct parents. One doesn't necessarily have to back-merge to fix this. Reassuringly it appears to be purely a graph issue rather than any issue with the underlying commit history.