Sure, but they were on opposite sides for most of the time, and they inflicted horrendous casualties on each other (Germany suffered almost as many casualties in a single battle in the east as the entire war in the west, and Russia more so) and both committed horrible massacres on the civilian population of any neutral, conquered or enemy nation.
Given the numbers, saying Russia and Germany were on opposite sides in WW2 seems pretty accurate to me.
Why presume that the context of the game is the entire war? A lot of games and other media relating to the war focus on specific points in the war, and so your last statement doesn't necessarily apply to the game given the information conveyed in the article, specifically regarding the implication of historical inaccuracy.
Given the numbers, saying Russia and Germany were on opposite sides in WW2 seems pretty accurate to me.