If we run mk_prepare_ligand.py on this test SDF:
https://github.com/forlilab/Meeko/blob/07a38f8bac4aa9eef4ef30aa8e67475b15d517aa/test/rdkitmol_from_docking_data/small-02_five-deuterium.sdf

We will get:

REMARK SMILES [2H]O[C@@]([2H])(C[C@@H]1C[C@H](O)C[C@@H]1[2H])C([2H])([2H])[NH3+]
REMARK SMILES IDX 3 1 13 2 16 3 5 7 6 8 11 9 7 10 10 11 8 12 9 13 2 15 1 16
REMARK H PARENT 16 4 16 5 16 6 9 14

Only four polar hydrogens are listed in H PARENT. There should be five. The missing one is the polar hydrogen isotope that is also the first atom in Smiles. The information went to SMILES IDX: (at the end) 1 16.

This looks like an unexpected behavior. planning to fix in #296