I also read an article in Zaman where several Turkish activists claimed that Israel was firing on them with live ammunition before the commandos dropped on board. In the confusion and excitement I can easily see how being fired on with less-lethal rounds from the air could be mistaken for an actual attack.

'Israelis opened fire before boarding Gaza flotilla'

The Israeli commander seems to verify that the Israelis were firing warning shots and stun grenades before they came aboard.