My WordPress theme got soft rejected twice fro the same reason (among others) by the same reviewer, for an unzipped plugin (revslider) in my theme plugins folder, used with TGMPA.
Here is the last screenshot that reviewer provide me:
As far I see, all those warnings occured because the reviewer unzipped the Slider Revolution plugin (revslider.zip) in this location mytheme/inc/plugins/, perhaps to make sure I providing the latest version of it, then he run the Theme Check plugin.
My theme does not contain such a bunch of issues using Theme Check.
What should I do? I send him a message when I resubmit my theme but no results.