Use the report a problem function of the site and word your complaint strongly. Tell them this is a different problem from the Superman I/III issues, so it does not fall under the "report to Warner" standard reply they've been giving.
This has happened to me with Amazon in the past, where a boxed set contained a duplicate disc and as such, a missing one. Word your complaint such that you make it clear you just want one disc replaced, that way they'll know you're not someone who likes to take advantage of their customer service and get duplicates of titles despite their being intact (which happens a lot if you read some of the atrocious posts on these boards from people who even indirectly brag about doing it).
Mine was worded something like: "I DO NOT want a replacement set, I have no use for it and it will just add clutter to my home. I just want you to send me Disc 2. If you would like, I will send you back the duplicate Disc 3, then you can process my request after you've received it. I can send it by registered mail."
Their email told me they cannot send single disc replacements for boxed sets, and to just keep the incorrect set with their compliments and their apologies. When I received the replacement set, it was actually UNSEALED, and had a handwritten Post-It stuck on the top: "Opened for inspection purposes to confirm proper disc contents."
Let us know how it works out.