I was playing my copy of Let's Go Eevee, and caught three Eevee on Pokemon Road. One I evolved into Vaporeon, one I evolved into Jolteon, and the other I evolved into Flareon. Before doing this, I checked my Pokedex and saw that I had not caught or registered those three Pokemon before. I then placed the Vaporeon in the Pokemon Daycare, and left to try to Catch Combo Magikarps to find a shiny Magikarp. After I found one (yay!) I went back to the Pokemon Daycare. The lady said my Vaporeon had gained a level (getting it to Level 40) and I took it back. When I went into my Pokemon Box, there were suddenly two Vaporeons. One was at Level 40, and the other at Level 39. Both had the same moveset, and almost identical stats.
Please note that I have never traded with myself or anyone else, never caught more than those three Eevees (apart from the one at the start you are required to catch) and I do not play with cheats. How did the second Vaporeon get into my game?