That's certainly a bug, one that I haven't heard of before... I actually can't think of what could cause it, the level progression works off of GameMaker's room order (using room_goto_next() for most of the levels). It's possible that going into endless mode first or some weird combination of room switches I haven't thought of would cause this, as score and text popups are currently pretty broken for these reasons.
I understand that you probably wouldn't want to go through the whole thing again to see it, so I threw together a Boss Hotfix patch version which replaces level 2 with the boss if you wanted to give it another shot:
Sorry for the trouble!