Also witnessed this several times on Turkish Airlines. On flights to Central Asia ex-IST, I have even seen people plunking down straight into a business class seat when boarding, only to be moved on to their assigned Y seat when the actual seat holder arrived with an FA in tow.
I chalked it off to a combination of mentality (let's if I can get away with this....) and inexperience. Some people you see in TK Y cabin may simply not fly very often and may think "hey this seat is empty, I am not taking it away from anyone, what's the big deal?".