You may have file or directory ownership or permission problems. Sometimes when FTP or SSH shell transfer of files are made, the permissions or ownership settings are improperly set. The user and group ownership should be set to yourdomain:yourdomain (root without the .com/.org) and the permissions as per general rules. Instructions can be found on several sites by searching for WordPress permissions and ownership. You can also find scripts and wordpress plugins that say they will fix this for you. I have not tried any of these so I can’t suggest one.
Similar to Apple IoS or Windows, lack of proper permissions and ownership can prevent the ability to overwrite existing files and folders, thus preventing installation of plugins or updates.
