I was playing Mauve Manticore 6 with friends and when we completed the third section they got taken out to claim their loot however I was taken back and my only option was too replay mission 3.
Did they leave your team or dismiss you from the team before you had a chance to take your loot? That will stop you from getting it. It's a known bug http://forums.cardhunter.com/threads/2-co-op-bugs.7601/ , fixed in the next release. http://forums.cardhunter.com/threads/test-build-3-50-0-29-july-2015.7741/ You can email support@cardhunter.com, I think they might be able to restore your loot. Please include your game account name in the mail.
The only notable thing was that I had died and I was sitting watching the others play, but other than that nothing odd had happened during the play through. I will try emailing support though, thanks!