Also what happened to Soviet soldiers that willingly deserted and joined the German side? Were they just placed with other Soviet POWs and shot or transported to open air camps to die of cold, starvation, and illness? Or sent to work as forced laborers?
Many soviet soldiers who deserted to the German side were used as anti-partisan units, camp guards, and to a lesser degree as front line troops. The Cossacks are a example of a ethnic group that was singled out by Stalin's policies and along with Ukrainians who willing volunteered to fight against the Soviet Union.
The German invasion of Poland was planned and cooperated along with the USSR, this was one of the agreements laid out in the Molotov-Ribbentrop pact signed on August 23. While this does not exactly match your question on soldiers fighting side-by-side, the Soviets and the Germans did fight against a common foe and were allies.
They even had a Soviet-German parade! http://en.wikipedia.org/wiki/German%E2%80%93Soviet_military_parade_in_Brest-Litovsk