I'm doing the strictly business quest and was enslaving Susan Lancaster, as it's a bit tricks I saved before using the mesotron on her, after finding her alone in a bed for once. I shoot her while sleeping and ask her to put the collar on, she leaves but shout on the guards who become hostile so I reload.

Now Susan Lancaster is gone to paradise falls so I'm pretty dumbstruck as at the point of the save she should be sleeping in her bed, but as she is at paradise falls I might get a success on the quest even if I have the collar in my inventory, arriving at paradise falls I see that she is moving south. Fast travelling back to Tenpenny tower I'm able to intercept her and successfully enslave her in the wilderness north of the tower where nobody sees it.

Has anybody experienced something similar?

things like that happen to me. stun and color the target, only to have them shut for help. that is what stealthboys are for.

Not the scream for help part that is natural, I would do the same in her position
Problem is why was she moved to paradise falls after the reload?
It makes no sense at all.

some of the action must still be in ram when the reload was done so the program was confused.

Yes probably the collar instruction, character with collar will go to paradise falls. Since you can only use one collar at a time it was probably a sort of global constant outside the savegame, the savegame is basically a mod as I understand.
It caused no problems and made the capture easier for me, might be reusable for other characters.