Possibly it was saved, being a piece of Divine Pharaoh, somebody remembered
it at the last minute, the mummy was already wrapped so they popped in a convenient
canopic box, just to make sure. Or possibly it was put in the pre-prepared canopic
box right after extraction? Presumably it would be considered important that
it went to the grave with her - can't have a Beautified Osiris missing a tooth
can we?

It does seem kind of improbable that a tooth almost exactly matching a missing
one would 'just happen' to be in Hatshepsut's canopic chest.