You can have two Gotenkses if you have Goten, Trunks, and Gotenks in the same team as well. If you decide to have Gogeta or Vegito with Goku and Vegeta on the same team, you can potentially have two Gogetas and two Vegitos. Fusion characters have their own slots in 2.

Given that it's Super Saiyan 4 Gogeta, it's probably intentional. This was fixed in 3, where beams can now struggle with ball attacks.