The only things I can think of are
- You are misremembering something. Maybe it was a different Pokémon you saw, or you battled someone with it (although I looked and didn’t see any trainer in Leaf Green with a Murkrow...) Or you played someone’s Fire Red and conflated the two.
- Non-genuine cart with a hacked ROM has exclusives from Fire Red added.
- An unknown/undocumented glitch caused you to encounter it.
The latter two seem unlikely and the first one seems most plausible to me. I don’t mean any offense and I’m not trying to call you out. Just feels like the most likely explanation.
The games don’t forget which version they are so that can’t be it. It’s not a single ROM that gets marked as red or green, each game is compiled and built to be what it is on the cart.
Other than that I really can’t think of what it could be. I agree, searching around online I haven’t found anyone or any glitches to explain that happening. Weird!