Regardless of aftermarket parts, sure that does have allot to do with it however, what type of intercooler did you install? I'm assuming it's a front mount? If so, I cannot give you an educated answer to what should or should not take place, because a few things are working against you. If it's a front mount and you attempted to cram the largest intercooler in there without checking concerns of rubbing under normal engine flexion/load etc. well, I know you don't want to hear it, but thats your fault. I'm all for aftermarket parts as well as the Mazdaspeed parts, but I certainly would never install any one size fits all part to include an intercooler. Why? because of what happened to you. There's way to many parts to be damaged to include your warranty if it's not application specific. For your sake, I hope things work out, but I also hope it's a lesson well learned. Lastly, remember they have to prove the aftermarket part was the cause of the failed part(s) and again I hate to say it, but just from reading this, it appears that way.
Good Luck!