Well this isn't exactly a Pokemon dying, it is the death of what is essentially a Pokemon
*That makes absolutely no sense
Hear my out: this is Yamask's pokedex entry from White and BW2:
"These Pokémon arose from the spirits of people interred in graves in past ages. Each retains memories of its former life."
Yamask has died at one point, and is now, essentially, dead.
There is also an instance where a Pokemon's death is mentioned, but not in its own pokedex
Tailow's Sapphire entry states:
"Taillow is young - it has only just left its nest. As a result, it sometimes becomes lonesome and cries at night. This Pokémon feeds on Wurmple that live in forests."
As shown here, Taillow kills and consumes Wurmple regularly.
Similarly, Heatmor's white pokedex entry states
"Using their very hot, flame-covered tongues, they burn through Durant's steel bodies and consume their insides."
Ouch. Yup that's pretty much it right there.
So yes, there are other instances of Pokemon death mentioned in the pokedex, but typically they are not as direct as charmander's or spoink's, There may be more than these as well, but hope this helps.