Was there overstocking on Kazakhstan flight?

Forty nine heifers died on a flight to Kazakhstan on 22nd/23rd Oct 2013.  The cattle were all on the top tier of a two-level crate configuration. Reportedly the 747 freighter's air conditioning system malfunctioned.

However, according to Kazakh news service Tengrinews, Almaty Oblast chief veterinary inspector, Omirserik Kydyrbatev, said infringement of animal air transportation rules caused the cattle to suffocate.

Given the photo published by the same news service (presumably from this shipment), one wonders whether stocking density was an issue...it is odd that only animals on one tier were affected and that a veterinary inspector reportedly commented that infringements had occurred.