User blog comment:Reptileman778/What is the canon explanation for why you are fighting geth in multiplayer?/@comment-4953843-20120910172117/@comment-2127131-20120910193129

If I had to say. They didn't connect to the main Geth network so they didn't just the update.

I'm basing this on what (True) Legion said during its Loyalty mission about how the virus would work if it was rewritten.