I've tried searching for duplicate reports of this, but so far I haven't been able to find one that mentions this exactly. Hope I'm doing this right.
The server/world is new and generated with version 5.0.1
Only generation 1 & 2 have been enabled (ever) on the server.
However, the Haunted House (spawn block) still spawns Lampent and the trainers also use Pokemons from other generations. However the world spawns are fine.
I saw another bug report that mentioned traders tapping into disabled generations, but so far I have not met one that does that.