What to check
Charmander’s four documented kit moves are Special. Bulbasaur and Squirtle have mixed kits. Check the moves you actually have in the run, rather than the species alone.
PokéBonk — Why does an upgrade say that none of my moves use it?
The short answer
Read the upgrade’s affected-move list. One observed Protein offer increased Physical damage while explicitly warning that the current moves did not use it. Match the upgrade to the damage classes shown in your current kit.