I read this story a couple of years ago but can't seem to find it since.It's a short story.
The story starts with a programmer debugging a program and not being able to find the bug. Frustrated, he decides to disassemble the program and look at the assembly and found instructions that can't possibly come from the original source code. He then looks at the compiler for the source of the bug and even recompiles the compiler but the alien code still managed to make it into the program.
Then he decides to actually see what the alien code does and finds that it's trying to do something simple like adding two numbers but doing it in a completely non-intuitive way. He concludes that no human would do it that way and starts suspecting a virus.
Later he finds alien code everywhere from the compiler (not in the source of the compiler) to the assembler to the OS down even to the router in his office at which point he begins to suspect that the alien code may even be part or the CPU itself (modern CPUs after all are designed on computers).
The story ends with the programming team receiving a letter from another engineering team (I forget if it's Geneva or Tokyo or somewhere else) stating that they've found the same thing but every effort they've tried to publish their findings got censored by the emerging AI (hence the handwritten letter).