I just opened my copy of Batman Complete Animated Series that I ordered from DD and both spindle that holds the discs to the case are completely broken off.

Should I contact DD and/or Warner about a replacement or should I get replacement cases? I'm not sure if the original rumors of this set being limited are true and if they are I would rather not risk sending it back and not getting a replacement. And if I had to find replacement cases, where would I even get them?

I'd contact DD first.

Go ahead and contact WB as well, couldn't hurt. I would imagine either of the two will help in some way.