I had the same issue and here is what iTunes Support told me to do:
Dear iTunes Customer,
Thank you for downloading the Season Pass of Mad Men, Season 6. You may have experienced issues with your episode downloads of "Inside Mad Men: The Flood" and "For Immediate Release". We have corrected the problem and a new copy is available to download, free of charge. To receive the new version, please re-download the title from iTunes.
Before downloading the new version, remove the current version:
1) Open iTunes on your computer.
2) Click on your TV show library.
3) Click the TV show to select it, and press the Delete key.
4) Click Delete TV show and then click Move to Trash.
To download the new version:
1) Sign into the iTunes Store.
2) Click Purchased on the right side in the iTunes Store under the QUICK LINKS section.
3) Click on TV Shows and select the TV Season you want to download.
4) Click the Cloud download icon next to the episode you wish to download.
You will now have an updated version of the TV show in your TV shows Library.
To delete and download the TV show from other devices, see http://support.apple.com/kb/HT2519.
iTunes Store Team
This worked for me. It's a bit of a workaround to say the least, as Apple should fix this on their end, but what can you do when you're wanting to watch one of your favourite TV shows.
I deleted my the iTunes library files as shown here.
Sure you have to re-import your library, but at least you can get your Mad Men fix on
Hope it helps.
I received a reply from Apple saying that they've re-added the episode to my account. When I reopened iTunes it started downloading "Inside Mad Men: The Flood" a second time, so I now have two copies of that behind-the-scenes video, and am still missing this episode.
It looks like the episode was never actually credited as part of the season pass: If I open the iTunes store on my iPad and navigate to Mad Men Season 6, it lists all episodes with "Download" buttons next to them. But the button next to episode "For Immediate Release" says "$2.99". A clean iTunes library on my Mac had the same problem – the episode wasn't listed as a purchase.
I'm beginning to think repucharsing it at $2.99 is a better option than dealing the ongoing saga of the missing episode.
After weeks of going back and forth with Apple support, I finally figured it out (for my case at least).
Apple Support kept on resetting the episode to have me re-download it. It would disappear as soon as the download was complete and appear as hidden on my account side in the store.
I eventually selected "Show Duplicates" from the View menu and noticed that I had two 105 - Inside Mad Men - The Flood. One was a few minutes and the other 47 minutes. Sure enough, the long episode was the mislabeled missing episode 6. I manually changed the info and it now lists properly.
Jers, above, was on the right track. Apple must have mislabeled it.