The more honest programs will outright tell you it's a keygen, and classify it as potentially unwanted program, but will still want to delete it. To this day, I still find key generators (which have no malware code at all in them) declared viruses or malware. They used to be really bad about this, with McAfee outright deleting files with the filename of keygen.exe, saying that it was an uncleanable virus, and that the file could not be cleaned.
The fact that sometimes a crack does have an actual virus or malware in it doesn't help. Windows Defender is one of the worst about this. The antivirus people refuse to fix this, because it opens the door for real malware to hide from the heuristics by masquerading as a crack, and because it's a nice dose of FUD to scare people into not pirating. This tends to set off false positives for heuristics. Most cracks nowadays need to use malware tricks to actually work.
