Order in the file directory do not match the block order

[Shonumi]

Looks like something happened to your memory card file that messed it up. The dialog gives you the solution. Export all of your saves to .GCI files, delete the memory card, start Dolphin with a game that makes a save (SSBM creates one right away, this step makes sure Dolphin creates a fresh, new memory card file), then import all of your .GCI files to the memory card file.