Took a while to figure this one out... only affected seemingly random users.
When modern standby is enabled on Windows the AnyConnect may receive several internal error pop ups
https://bst.cloudapps.cisco.com/bugsearch/bug/CSCvv69211
so when S0 sleep enabled laptop goes to sleep, while connected to VPN, when it comes out of sleep mode, users gets pop up "internal system error"
Hey, looka you! You got a bug for it!