This is not expected behaviour, at least for me. When saving a file (scripts/notecards) to the local computer's filesystem it silently fails when the filename starts with a tilde (~). It would be nice if it would go ahead and save it, but if that's not possible, could it at least simply refuse to save at all just as it does when there are slashes in the filename?
The log of the activity doesn't show anything unusual: If you need a full log I'll post one. It's easy to recreate, just create a notecard or script in your inventory with a tilde as the first character of its name and try to save it to the computer's filesystem.