A fairly minor one, but the revelation that Mr. Buu created a wife named Buuby and went on to have kids with her by shooting her with a "love beam" is either hilarious or idiotic depending on who you ask.
The game itself. Those who know about it debate its canon status as frequently as they do GT. Specific elements of contention include the prevalence of the Super Saiyan transformation, and New Namek and Yardrat's destruction. This has only been exasperated with the release of the Xenoverse games, which uses the characters, setting, and plot points of Online but in a different context, muddying the waters further.
All Human players actually being saiyan hybrids descended from Goku or Vegeta is also one. Particularly for players who wanted to play as actual Humans without alien lineage or didn't want to be descended from Goku or Vegeta ( Word of God however has established that pure humans are still the weakest race, so the decision is justified somewhat).
Character Tiers: Namekian Shadow Knights in particular were considered the best PVP class. Other High Tier classes were Swordsman and Dende Priest for PVE. On the lower end, Turtle Hermit wasn't considered that useful, and inferior to Crane Hermit in most aspects.
Ensemble Dark Horse: The Majin race was the best received idea of the game, to the point they even made it into Dragon Ball Heroes!
Surprisingly Improved Sequel: Several plot elements are considered to be better than their equivalents in Dragon Ball GT by fans. It helps that Goku and Vegeta presumably met their end in a blaze of glory befitting two Saiyan warriors rather than whatever that was at the end of GT.
They Wasted A Perfectly Good... Everything: The game was shut down before a lot of elements could have been expanded on. The Mechanic classes, Cell's clones and descendants, Miira's plans, all those had merely passing mentions before the end. That's to say nothing of the character creation system, which after the shutdown left only the generally-loathed Ultimate Tenkaichi as an option for those with Alt Itis.
It seems that the people making Dragon Ball Xenoverse are looking to subvert this, what with the superior character creation as well as the recycling of several characters and plot elements from Dragon Ball Online.