@batman
I had this problem so I feel your pain. Unfortunately, the scrape sources for games on the RetroPie can pull down videos that aren't encoded in a way that EmulationStation can run properly.
To get by this I use Skyscraper to download everything and build the Gameslist.xml file.
Then I go to: https://emumovies.com and get them from there. They are encoded perfectly and work great. They are a good resource for everything really.
I would recommend creating an account, then you can use their FTP server to download everything easily. - https://emumovies.com/ftpdetails/
Once you do that copy and replace your already downloaded videos with these. I literally just did all of this during this week for my MAME collection so I know it works and it will help you out.
It would be cool if the RetroPie could use them as a Scrape source.