In Jmol 11.9.20_dev, the transfer of a terminal alkene or a primary
amine from both Marvin Sketch and JME followed by minimize
addHydrogens results in coincident hydrogen atoms. Both hydrogen atoms
are in the molfile, they are just coincident. There may be other cases
of coincident hydrogen atoms, but these two general cases quickly
caught my attention. It probably goes without saying, but allene and
ketene produce the same result.