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.
I don't think this means there are back doors. I did find it amusing Jacob Applebaum hung around in Berlin pretending to be in exile because of American repression while being paid a $100,000 salary by the State Department, funneled indirectly through the military industrial complex.
Source: https://pando.com/2014/07/16/tor-spooks/ (I think Pando's core facts are correct but some of their conclusions are overblown)
Edit: mixed up CIA and State Dept
The Internet is operated by Internet service providers, not DARPA. The U.S. government role in directly operating the Internet ended in 1995 with the shutdown of NSFNet. The ISPs buy hardware from private companies that implement the public Internet protocols.
That doesn't mean that there aren't backdoors of various kinds in Internet infrastructure, but whatever backdoors exist aren't likely to exist by virtue of DARPA's role in funding the original research.