This bug has been in the game since 2003 and while it doesn't happen every time, there are certain situations in which it will occur. It occurred during the 2006 playoffs, and it has occurred again this year as well. (see below)
Here are the seedings for the NFC Playoff teams this season.
1. Atlanta Falcons (13 - 3)
2. Chicago Bears (11 - 5)
3. Philadelphia Eagles (10 - 6)
4. Seattle Seahawks (7 - 9)
5. New Orleans Saints (11 - 5)
6. Green Bay Packers (10 - 6)
Wild Card Round results
#4 Seattle defeats #5 New Orleans
#6 Green Bay defeats #3 Philadelphia
So in the divisional round, #1 Atlanta will play the lowest seeded winner from the wild card round which is the #6 Green Bay Packers and the #2 Chicago Bears will play the highest seeded winner which is the #4 Seattle Seahawks.
However, if you sim these exact results (regular season AND wildcard round in Madden 11) and you will see that in the divisional round, Madden will put Seattle against Atlanta and Green Bay against Chicago, which is wrong.
This situation last happened in 2006, and Madden was wrong then as well.