Basically, I just ran a scan of my computer with Malwarebytes (updated the definitions before running), and it said my \"helloworld\" program written in C# has a trojan.
The answer by Baldrick is likely correct, but there is also another possibility: There are viruses which search for random executables on the system and modify them by inserting their own code into them (this is, in fact, the original definition of "computer virus"). When you find that an executable which you know is trustworthy suddenly is reported as infected, you might be dealing with such a virus.
But unless your virus scanner reports other executables as the same virus, this is unlikely.