It's normal behaviour to see the files of both version present on the drive after an upgrade.
In v12.1, SEP takes a side-by-side approach to upgrades, and silos all the files for the new version on the drive before swapiing the files and drivers around on reboot. The older client's files are then removed afterwards (generally when the client isn't doing much).
You can test this out, just perform an inplace upgrade and give it a few hours, the old client files will eventually disappear