When Piranha Plant launched for Smash Bros. Ultimate, some users were complaining that their save data was corrupted after using the character in All-Star mode. Nintendo was aware of those complaints, and looked into the situation right away. The thing is, Nintendo can't seem to replicate the problem.
“We are aware that some users are posting about possible issues with the latest Super Smash Bros. Ultimate update. After extensive testing, Nintendo has not been able to confirm that there is an issue, although we will continue to investigate and monitor the situation.”
Whatever is causing the save game corruption seems to be impacting a very small number of players, and whatever is causing the issue escapes Nintendo at this time. Maybe it's some other weird set of circumstances for those select Switch owners, and it has something to do with content outside of Smash Bros. Ultimate.