Has anyone else had this happen when you console in some NPC's just to mess around with and later they respawn back again?

I used the console code to add 3 raiders just outside Temple of the Union to test out weapons on (after that quest was done) and when I fast traveled back crouching in the CSA those same 3 raiders had respawned. I remembered this is a trade caravan stop and they could easily attack the caravans so I consoled in 3 Talon Company mercs to take them out which they did. I just hope these guys don't attack the caravans when they come by.

After this I've been going to remote areas for frapping weapons tests on different NPC's because I don't want duplicates wondering around where they might mess things up.

Well since your console command is accessing data from an esm . Im sure its adding all the properties for that particular NPC ID.
And that would include respawning data. If you dont want them to respawn , youll have to access them in the geck and change it ,find one that doesnt respawn (use thier base ID) , or create a new one that doesnt respawn.
But Im sure removeing them with the console command would do it also.

An alternate method would be loading a save location to before you added them with the console command.