I am not clear on the problem you are facing. Do you see that there are DENY permissions applied on the database objects? From a user’s perspective, when they are not able to access a database object, they wouldn’t know whether it is because there is a DENY or whether they don’t have access permissions.
First look at the login the client is using in SSMS object explorer. You can see this under the Server -> Security -> Logins node. If you right click on the login, you can see what permissions and roles they have.
Also, if you suspect there are denies on one or more objects, check which groups and roles have permissions denied on that object.