The Corriere della Sera claims that the same aircraft (unclear whether it was the same flight crew) was involved in an incident a couple of hours earlier on the outbound leg (Rome-Pisa), getting too close to another aircraft as a result of misunderstanding a clearance from Pisa ATC. No more detail than that as yet.
The captain is said to be "superlatively experienced" 15,000 hours total; 9,000 on type; an ATR 72 check pilot. He spent most of last night being interrogated by the Italian fuzz.