Noticed this for the last few releases and is still an issue at 11.5
I have a synchronised folder which i dont wont to sync the subfolders, so i have under Filters->Exclude Filters "Exclude Filters" checked
with this set, if i go back later and DONT go to the exclude filter, and just hit Ok from the "Include filters", it adds all the subfolders that i had previously told it to exclude
I can work around this at the moment, but would be good to get it fixed at some point