Hello Czql5v,
This may be related to the behavior reported in the next article, where some permissions are not applied for items, but they do for folders:
As recomendation, the command line to mirror the persmissions iand keep the trees aligned would be:
ROBOCOPY <source> <target> /MIR /SEC /SECFIX
--If the reply is helpful, please Upvote and Accept as answer--