I've noticed that too.... but--- dont have 3 duplicates... only 2.... see below
Example 1.... I take a pic with Instagram itself.... Ill filter it... and upload to Instagram....
"My Gallery" stock app, "Gallery Pro" (i prefer Gallery Pro), and Astro File Manager shows the filtered final product pic I took on Instagram in the Instagram folder (again--i use gallery pro) and in the original unfiltered pic in the Camera Folder (since Instagram uses the native camera and it saved in the DCIM folder by default just like all camera pics---so i assume). No other "3rd" pic is shown anywhere... so I have 2... Not 3 like you state..
Example 2........ I'll use a previous taken pic from Camera or Camera FX app... or I use a previous pic like a MEME.... in this case, I used a previous pic on my daughter taken 1 month ago.... Ill filter it... and upload to Instagram....
"My Gallery" stock app, "Gallery Pro" (i prefer Gallery Pro), and Astro File Manager shows the filtered final product pic in the Instagram folder (again--i use gallery pro) and in the original unfiltered pic still in its original "Panama City March 2012" Folder. No other "3rd" pic is shown anywhere... so I have 2... Not 3 like you state..
I would go to Apps>manage apps>instagram.... wipe cache and data... then uninstall the app.... power down the phone... wait 3 minutes... power up the phone... reinstall instagram... re-login to your instagram account with your username and password... and try a new pic uploaded again..... if you still get the same 3 pics (original pic in camera/DCIM folder, original pic in instagram folder, and filtered/uploaded pic in instagram folder), then I would contact the devs at instagram and report the issue