The cutout the lower sheet through the top sheet is performed incorrectly. The cutout is done in a different site than the overlapping plates. Function Component Modification> Common> Boolean subtraction
After running some test, found that plate ECS are placed far away from plate.This may be the raison why Boolean subtraction are not been done correctly. Recreating those plate in the same model works fine and the ECS are placed correctly. have send a email to user to setup a live meeting.