It's not Tobi's AI targeting, but rather the order in which your characters are using their ults while on Auto. I run into the same problem all the time.
Basically, in ranked and in any kind of "AUTO" setting, characters with damage-based Ultimates (Tobi, Naruto, etc), will always target the lowest health character on the opposing team, regardless of if there are better choices.
However, once that character dies, any of your ninjas who were set to target them will instead use their Ultimate on whichever character is directly across, in line with them. And since all characters pick their targets simultaneously in a large team battle, it often results in Ultimates being wasted on clones and summons, as they stack in front of the actual ninjas.
Not a bug, and not really a design flaw from the devs perspective, but definitely annoying for us. It's why your positioning matters way more th*ual when in ranked, so you don't have that situation happen as often.