Are you dropping a round in the chamber and trying to close the bolt??
The mauser type actions---1903, Arisaka and others---are "controlled
feed". If you want to do a single shot, push the round down into the
magazine and let it feed up the bolt face and behind the extractor hook.
You can bevel the extractor so it will snap over a chambered round, but
a ummodified stock extractor will have a difficult time doing it.
Yes--I know this kind of goes against the reason for a magazine cutoff.
I don't have a good explanation!