This is a base game issue not related to ss2 except the fact that it can occur With ss2 plots. Like kinggath said turn off auto city upgrades and turn the plot upgrades to on visit upgrades. Also don’t fast travel into a settlement that has ss2 plots or city plans then fast travel to an interior workshop cell after.Do you plan on releasing patches for the time being on OTHER bug fixes? (specifically the city plan objects being cloned into HQ?)
as far as fixing it unless you know how to recode the engine I’m guessing there is no fix that can be done externally.