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.
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