My phones have same issue i don't know if i do something wrong or what but after I connect my phone to pc and upload some files you are not able to see them on phone.
Example i upload new.apk to Downloads folder and disconnect my phone. Then going to Download folder on phone but file is not there. However if you go trough file explorer you can see file there. Also same issue if i connect phone to pc and delete files. After disconnect and going to that folder files are still there but if you go trough file explorer wont be there.