Random encounter triggers rely on a script state to determine whether or not they are currently in use or if they are available to spawn new encounters. This state does not persist through a cell reset, which creates an edge case where multiple random encounters can spawn from the same trigger. In the base game, most random encounter triggers are flagged to never respawn in order to prevent this. However, all random encounter triggers added by DLCs are allowed to respawn.
As is often the case, I just posted a mod that explains and fixes the issue. The unofficial patch would be fine to include the changes if you wish:
https://www.nexusmods.com/fallout4/mods/107194