That would be "Pictures Don't Lie" by Katherine MacLean, although based on your description I believe you're thinking of the 1962 TV episode based on the story. The reviews here mention all of the plot elements you describe.
Something's wrong! The aliens claim to have reached our planet ... yet
they don't see anyone waiting for them, and the waiting humans don't
see the alien ship. Now the aliens claim to have landed in an ocean of
noxious chemicals, and they're being attacked by bizarre monsters.
Angrily, they accuse us of lying to them. The transmission fades as
the 'monsters' (from Earth, apparently) destroy the aliens.
Eventually, the Earth people suss out what went wrong. Although the
aliens look like humans, they are in fact much smaller than we are:
microscopic, in fact. Their tiny spaceship landed in a rain puddle,
where it was devoured by protozoa