In Generation I, Acid Armor caused the user's sprite to become invisible until it fainted or switched out, or the battle ended. In later generations, the user's sprite does not become invisible.
Additionally, in the anime (oh hey what a coincidence it’s also a Vaporeon)
Vaporeon jumps into the water, glows blue, then disappears. It can then swim through the water as if it were invisible. Seconds later, it jumps out of the water and attacks the opponent.
So it likely was intended, but knowing how broken Gen 1 was it might not have been. But the point is, it happens to everyone.
Oh yeah, sauce.