If this was an SA-17 type Buk launcher it is able to detect transponders and determine if it was a civilian aircraft. Reports so far say it was this type so this rules out auto-mode being used, it also strongly suggests the operator was not fully trained.
The SA-17 wasn't developed until long after the fall of the USSR, IIRC Ukraine only has SA-11 systems, mostly Buk and a few Buk-M1.