WordPress Automatic Plugin Update Renames Plugin Directory

It turns out the answer was simple I didnt have my plugins content in a subdirectory slug inside the zip file
eg.
I had :

my_plugin.zip
   |- my_plugin.php
   |- admin
        |-admin.php

I should have had 

my_plugin.zip
   |-my_plugin
        |-my-plugin.php
        |-admin
            |-admin.php

Once you add that sub directory the auto updated will work as expected

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