Actually I am rather sure that it has to do with stock game and wasn´t introduced by any of the mods (as I don´t use any mods that mess with the mission system):
I got a mission to rescue a Kerbal from Kerbins orbit
After accepting the mission I discovered, that the ship of the Kerbonautr to rescue wasn´t in Kerbin orbit, but rather on a suborbital trajectory around Mun.
I think what happened was, that the RNG placed the ship (and its orbit) too close to Mun, so that it got into Muns SOI and therefore the ship, immediately after creation, got captured by Muns gravity
See here: