That is not a glitch but an unfortunate inconsistency in where the objects are anchored. Whereas rectangle objects have their origin in the top-left, the tile objects have their origin in the bottom-left (or even bottom-center, in the case of isometric maps). At some point in the future I'd like to unify all this.
Probably. There's a related issue on GitHub about having the anchor in the center. I'm just not sure exactly where to put this option yet.