Again, thanks to Hussein for this, from Kooora forums and other online sources.
Refereeing mistakes in favor of Milan (only major ones)
1. Milan 1 v 0 Inter (Ronaldinho’s winning goal)

2. Milan 1 v 0 Siena (Kaka’s penalty, just see how softly Inzaghi went to ground without being touched)

3. Atalanta 0 v 1 Milan (with the score at 0-0 Maldini trips Floccari and nothing is given)

4. Milan 1 v 0 Chievo (the Chievo player trips Kaka outside the area and the referee awards Milan the spot kick, which Kaka converted successfully)

5. Milan 1 v 0 Catania (Kaladze’s hand ball and no penalty given. That happened in 2nd half stoppage time)

6. Milan 5 v 1 Udinese (with the score at 0-0 a clear foul on Maldini that deserved a straight red goes unpunished)

7. Milan 1 v 0 Cagliari (Inzaghi pushes the Cagliari player into his keeper and Seedorf slots home)

8- Napoli 0 v 0 Milan (Hamsik denied a valid goal for a false offside flag)

9- Chievo 0 v 1 Milan (Chievo denied a valid goal for an offside call. Although two players were in an offside 'Position', they did not interfere with play or cause an offside 'Offence' as per Law 11 of the game)

Refereeing mistakes in favor of Juventus (only major ones)
1. Juventus 4 v 2 Milan (with the score at 0-0, Juventus is awarded a penalty which Del Piero converts for 1-0. As you see he was offside when the play started)

2. Atalanta 1 v 3 Juventus (Del Piero’s first goal came from an offside position on Marcheoni)

3. Atalanta 1 v 3 Juventus (with the score at 1-2, Marcheoni brings Floccari down and no penalty)

4. Catania 1 v 2 Juventus (with the score at 1-1, Marcheoni handles the ball and nothing is given)
5. Juventus 1 v 0 Fiorentina (Gilardino’s goal cancelled for a non-existing offside)
6. Juventus 1 v 0 Fiorentina (Jovetic denied a clear penalty)
7. Juventus 2 v 3 Cagliari (with the score at 1-1, Molinaro couldn’t keep the ball in and crosses for Nedved to score. Thankfully Cagliari managed to pull level and win the game later)
8. Genoa 3 v 2 Juventus (Nedved elbows Mesto and splits the poor guy's head open. The referee doesn't notice it, otherwise it would have been a straight red. I think even a yellow would have been enough for him to miss the Derby)
9. Genoa 3 v 2 Juventus (Del Piero dives and gets a completly non-existent penalty even after the assistant referee signalling for a corner kick, and Ferrari is booked for no reason)
10. Juventus 1 v 1 Inter (Legrottaglie fouls Zlatan in the penalty area, but the ref does not award a PK. 30 seconds later, Juve score)
Mistakes in favor of Inter.
1. Siena 1 v 2 Inter (Maicon's offside goal)
2. Bologna 1 v 2 Inter (Adriano hand ball before Cambiasso scores)
3. Inter 3 v 3 Roma (Balotelli’s penalty)
Note - Inter 2 v 1 Milan (Adriano’s hand ball) - Highly publicized in the media, but as per the laws and
subsequent statements by Collina, this was obviously unintentional, and a valid goal.