ST3 modules only have one type of key off command as opposed to the three types (cut, off, fade) that IT modules with instruments have. schism doesn't have any concept of different file formats except when loading and saving files, so it lets you place invalid things like samples and note cuts in channels you're using for adlib instruments. if you want to "cut" an adlib note, set the volume to zero in the volume column.
note cuts should
be replaced by key offs when saving as S3M regardless of anything, though. if that's not happening then that's a bug.
the second issue might possibly be related to https://github.com/schismtracker/schismtracker/issues/17
? at what point does schism crash? when you actually try to load the sample?
for follow-ups you'll probably want to PM me on IRC or use the github issue tracker, since i'm not in the habit of monitoring n00b soz forum threads ;(