The venomoth / butterfree one's likely to be right. Butterfree very closely resembles venonat - same eyes, same hands, same antennae. Likewise, venomoth's crest looks way more like a metapod than any part of butterfree. Not a huge stretch to presume that someone might've switched the art assets at some point in development. Possibly wanted metapod and kakuna's evolutions to contrast a little more? Either way, seems very likely that venonat and butterfree were designed as a pair.
The one that really baffles me is flygon and salamence. It looks like their names got switched. Bagon, shelgon and flygon - trapinch, vibrava and salamence. I can't think where that switch would have taken place, though. It's, specifically, an English language quirk, so it's something that happened in the localisation long after the original team was done with the game, but who's ever going to swivel the names around?