Overall I've not had too many major disappointments with the projects I backed. I can only think of two off the top of my head:
1. There are some disappointments to be had with Shadowrun Returns. First was the DRM snafu, primarily because they mentioned the licensing/rights issues -after- the fact, when it really sounded like there wouldn't be any problems. They gave everyone three Steam keys, which didn't do much for me since I don't use Steam. Fortunately, they released the game on GOG, and provided backers with a GOG key as well. Now if only they'd fix the broken USB dog tags...
2. There was a Firefly USB flash drive project wherein the appropriate licenses were acquired, so everything was moving smoothly. Then Fox comes along and cancels the project. Apparently Fox owns the rights to Firefly, and even though said rights were properly licensed, their legal department claimed to not know what a Kickstarter was, and pulled the plug on the project. Crazy stuff.