If DARPA created the internet aren't there are all sorts of backdoors and systems we don't know about built in? I've never really understood - if you can - those fundamentals.
All that really remains is that one or more governments have secretly broken essentially all crypto. Which is possible, I guess, but unrelated to their developing the Internet. There's a non-zero chance there are shenanigans going on with some root cert servers for SSL encryption, which require trust for their related identity-assurance schemes to work properly, but again, that's not related to government development of the Internet.