Wouldn't be surprised if it was due to engine issues or whatever. Smash Run has a scrolling stage and blastzone that depends on player movement. "Depends on player movement" is probably the key phrase since it'd make it difficult to code where the blastzone should be in case two players come across each other.
Yes, a solution would be to lock say the clashing players with a fixed blast zone, most locations within Smash Run are either walk-off or have potentially wonky platform placements. They might be able to create a compromise either with Ultimate's engine (Stage Morph) or a future game's, but I kinda doubt they were able to find one with the 3DS' relatively limited power.
Okay, I'm gonna try writing a potential codec convo:
Snake: "Wait, is that-?"
Otacon: "Yes, Snake. That's Cloud Strife. Ex-Shinra employee and member of the AVALANCHE revolutionary group. Logically he should suffer back pain from carrying that Buster Sword around, but he's genetically engineered by Shinra."
Snake: "Huh, I knew somehow that we have a lot in common. Thanks for confirming my suspicions Otacon."
Otacon: W-wuh-wai, how did you kno- A-anyhow, Cloud fights completely differently to you. He'll try to rush you down, use that sword's reach to his advantage and counteract your attacks with his own. He can also supercharge one of his special attacks when he enters his Limit Break state."
Snake: "Okay, this is starting to sound too much like Gray Fox."
Otacon: "His sword doesn't do a whole lot of shield damage though, and he can be a bit vurnerable when he's on the backfoot. Try to use those two to your advantage."
Cloud: "Hey, I can hear you two!"
Time to sit back and enjoy the show: