I think this "bug" occurs, when you get more than a level in a fight.
I had a great fight with wisp yesterday, which made me level 14, 15 and 16. So I could spend +3.
I skilled Ulti, stats, stats (in this order) so it looks like my ultimate was given for level 14,stats for 15 and stats for 16 - because I was level 16 afterwards I could skill ulti as my #14 skill in chronological order. Hope you understand what I mean.
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It seems the site doesn't recognize leveling up Wild Axes Melee form as leveling up the skill at all, and just dumps the fact. For example, in match 117688579, troll levels up Wild Axes Range at Level 1 (Ability 5509) while he levels it up in Melee Form at level 4 (Ability 5510). The site doesn't seem to be set to recognize 5509 and 5510 are the same ability, and makes it look like he got his ult at level 5, as seen here:
http://dotabuff.com/matches/117688579/skills