It quite looks like your Instagram script is appending the images to each ul and since the nav menu has a ul class in its structure the images appear there.
Try appending the images to a specific placeholder class with your script instead of the ul and let me know if that helped.
jQuery('.instagram').append(
Since you changed the place where the images appear from ul to instagram you now also have to create a div with instagram in your HTML.
Leave the jQuery like seen above.
See if the images appear only inside the newly created instagram div.
If they do place the instagram div where you want the feed to appear in your HTML markup.
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