Well this is certainly a problem, first we were getting banned for playing as Peach and now another new glitch has surfaced within Super Smash Brothers for 3DS which majorly affects online connectivity. Unlike that accidental ban for a couple days as Peach this latest shall we say game breaking glitch is leaving players banned for an unbelievable 136 years and if you can't do the maths to that you will very likely be dead by that point and the game be obsolete, not to mention this will leave you without a key feature in the game.
As it stands at this point how this glitch can to light or its origins are still unknown, but there are a few ways you can avoid this happening which are as follows:
A. Try not to target one player in Group/FFA.
B. Just use 1v1 for the time being
C. Don’t use online at all.
D. Don’t quit mid-match
Hopefully Nintendo will fix this issue with a patch sometime in the near future that will address this issue but in my personal suggestions to avoid a potential problem just avoid online for the time being and either play local or switch to another game until this problem is resolved.