The Italian, who was leading the championship just two races ago at his home Grand Prix in Mugello, is now fourth in the standings after crashing out at the last two races.
Baldassari has had a string of bad luck which was heightened at the Assen GP when he attempted to overtake Spaniard Marquez on Turn 4 to take the race lead.
The 22-year-old lost the front end of his bike and took down Marquez.
Baldassari’s leg was caught under his bike after the crash.
He was confronted by a yelling Marquez who proceeded to hit him.
Track marshals, who were not impressed by the behaviour, quickly stopped Marquez.
Baldassari went to Marquez’s garage after the race to apologise for causing the Spaniard to fall too.
The Moto2 riders exchanged words briefly, but it appeared that Marquez accepted the apology.
The crash resulted in both riders missing important points for the championship.
Baldassari has dropped to fifth in the standing while Marquez is now second in the championship.
The incident resulted in Spanish Augusto Fernandez, who was in third position when Baldassari and Marquez dropped off, to make his maiden win in Moto2.
He also jumped from seventh position in the championship to third.
The Moto2 championship is currently led by Swiss Thomas Luthi on 117 points, Marquez in second on 111 points and Fernandez in third on 92 points.
Catch the German GP this Sunday, July 7, at 10:00 pm AEST for the MotoGP category.