This is government 101. We tend to see governments as one big singular entity, this is rarely the case (and this especially true for a supra national organization like the EU with no real head of state). Instead you have different institutions with different goals that sometimes contradict each other. Then you have to account for multiple factions in those some institutions and you end up with what we currently have. The idea is that on the long run, if you average out the decisions/rules/regulation it is somewhat cohesive and leads to "good" governance.
