The 1.0.6 patch recently introduced Mewtwo in Super Smash Bros. for Wii U and 3DS last week. Unfortunately Nintendo had not anticipated some bugs related to the character, which explains this new update.
The arrival of Mewtwo on Super Smash Bros. caused some problems that were rather bothersome on each of the Nintendo consoles. Indeed playing Mewtwo on Wii U could erase the save game file and keep you away temporarily from connecting to online game modes. Complete 10-men Smash Mode after already finishing it with all the other characters could also reset the number of Smash Points.
On the Nintendo 3DS, some manipulations on the Smash Bros. menu resulted in a customization and Mewtwo whose attacks would crash the solo game could be ineffective or had effects at least singular.
It took barely a week to Nintendo to find where were the problems and correct them using the 1.0.7 patch that will automatically install via SpotPass. The update weighs small size of 21 megabytes on Wii U and 751 blocks on 3DS and only fixes bugs related to Mewtwo mentioned above.