Looks like this is due to the bonds being rotated to face the wrong direction and so the hydrogen renders inside another atom, which also causes problems with the example Molecules that get rendered for generic reactions in JEI, among other things.

I found:
Picric acid: additional methyl group (bottom)

This unfortunately happens with a few molecules. I don't want to fix it because the Molecule rendering code gives me nightmares.

i eated them (houngry)

Here is a list of all the molecules that I found missing a hydrogen:

• Acetamide (bottom carbon)
• Acetic Acid (bottom carbon)
• Acetic Anhydride (bottom carbon)
• Acetone (bottom carbon)
• Aspirin (top carbon, also hydrogen atoms are overlaping)
• Cisplatin (bottom nitrogen)
• Phenylacetone (top carbon, also hydrogen atoms are overlaping)
• Trimethylamine (bottom carbon)
• Vinyl Acetate (top carbon)