I'll throw something else out there.
It is documented that Rossi's riding style changed after the crash where he injured his shoulder. The point was that he couldn't go into the corners as late and lacked power on the changes in direction. He was making up for being slow into corners by trying to be quicker out which caused the tyre to spin more and led to Rossi stating that he didn't have the bike setup right. The trigger for this was his physical failing when in all probability, if he was 100%, he may not have had the particular issues above, more importantly he might not have had the spinning up on the way out of corners to the same degree.
The crash at Mugello was on a change in direction, at a high speed section. Let's say he came out of the first corner, was harder than normal on the gas making up for his failings, the tyre has spun more than it should, combine this with manhandling the bike from one side to another and it is no surprise that something could have gone wrong. Rossi himself said that he wonders whether his shoulder was a contributing factor to the crash. Seeing as we a microanalysing everything that happens in Motogp, maybe it was a contributing factor.