Either there is a miss communication or laziness.
Cause if they can blame it on aftermarket parts they likely would as this job probably requires them to remove the turbo's and replace them, assuming your turbo's are shot. Since they weren't sure if that would fix it, or didnt want to take the extended hours to diagnose, unsure if they would get replacement parts paid for from the warranty company, they likely just pushed the blame on you.
That's my theory given that I dont have both sides of the story, yet.
I know if anything I would take all aftermarket parts if I'm looking for warranty work, especially on big job's like turbo's.