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Computers of developers are compromised, so that the project deliverables contain malware or the project deliverables lack proper security measures.
Countermeasures: have backup copies at different machines, diff the different backups and try to use the classical intrusion countermeasures.
Developers get killed or tortured by the CIA or other agencies of various supermafias. (It does not even matter, if they do it secretly or totally publicly, because the mobs just could not care less.)
Countermeasures are missing. Usually the super-mafiosi, the professional politicians, do not care about civil liberties or human rights, as long as their salary is good and job secure and their job will always be secure, because in Democracy the one with the greatest campaign budget wins. However, there is a limit that the number of people working in the various supermafia security agencies is a minority, which sets a limit, how much other people they are able to kidnap and torture. Slaughterhouses for successfully killing hens, chickens, have been developed by private sector, but an automated torturing line, where people are tortured by robots like cars are manufactured in car factories assumes an IT project and it takes a bit of preparation to get it done and tested, so may be there could be some cooperation with private security firms, who would mount a sabotage attack on the torture line and plain physically blow up the equipment at the torturing plant. Most likely countermeasures that can be retroactively applied is to mount an assassination attack against the torturers/kidnappers and the political chain of command that, if not ordered, then at least allowed it to happen out of neglect. (The purpose of the assassination attack is not retaliation, but temporary disruption of enemy operations, like with bacteria, where the infection causing bacteria are never removed totally from the blood stream, but their amount is kept at a managable level.) If You think that this text here is a stretch, then please, please do try to remember, what other cases from the 2. World War and later history sounded like a stretch at first glance, but ended up being perfectly true.
Developers of censorship free communication tools are hunted down like weapons manufacturers and drug dealers. (Think of China, Soviet Union, etc.)
Countermeasures: legislation is always slower than technology development, so the infrastructure must be completed and distributed before its distribution and development becomes illegal.