Board Thread:Spoilers!/@comment-4877635-20140901190111/@comment-24674051-20141031162745

Really, the main thing that messes up Henry's family tree is Regina (go Figure). She adopts Henry, making Henry her son. But, as it turns out, She is Snow's Step-Mom, making Henry her (step) Great Grandson. This basically puts Regina at 2 positions on the Family tree chart, and some rather unusual positions at that.

The rest of Henry's Tree is "Normal" (ie, follows the expected chain). It's just a matter of who fills those roles that makes it messed up.