if everyone could play anyone, then the probability would be even across the board between the First and Second Place teams. However, there are two German teams in both the First Place and the Second Place and they can't play each other, then there are three English teams, (1 in 1st, 2 in 2nd), 3 Spanish teams, 2 French teams and so on.
Those 0% probabilities, where no two teams from the same home country can play each other, skew the other probabilities such that because of the MIX OF TEAMS that are in Group 1 and 2, there is a much higher probability that we will get some more than others, in our case it is Dortmund.
That doesn't mean that it will happen, just that there is DOUBLE to the chance of getting Dortmund as any other team we could get.
I hope that helps?