After you've set up advanced permissions, your users will only see the records and actions that are allowed by the profiles and roles they've been assigned to.
When a user can't see a record they need access to, or if they are able to see a record that they shouldn't see, check the user's profile and role in System Settings > Permissions and compare them to the record in question.
Compare the user's role to the record owner's role in the role hierarchy and compare the record type to the user's profile permissions. By breaking down each permission level, you can narrow down the issue and make the necessary changes.