The holes look like they could have very well been caused from shrapnel. Was the anti-aircraft missile involved one that explodes on proximity to the target?
A proximity fuse aboard the missile determines when it will detonate, creating an expanding fragmentation pattern of missile components and warhead to intercept and destroy the target.
http://en.wikipedia.org/wiki/Buk_missile_system
Explodes on proximity. Some holes in the fuselage might look like bullet holes (round), others not.
http://www.ft.com/cms/s/2/1d6a9ac2-10e3-11e4-b116-00144feabdc0.html