The incident, along with a failure to meet required fitness standards, saw the 22-year-old delisted by the Bombers on Monday.
New coach James Hird said SEN radio on Thursday that the decision to sack the son of former Essendon stat Merv Neagle came after players were told before going on leave in September that "things would happen that they wouldn't enjoy" if they returned to the club unfit.
"Jay didn't meet those standards and then something happened during training at one session and I said to him, 'There's a fork in the road for you Jay, and your career can go one of two ways'," Hird said.
"That's hard on Jay because he is a very good person who ultimately wants to be a very good footballer but he's got to prepare better than he's preparing for his career at the moment.
"When he comes to training, he actually trains very well but it's about more than that in footy now, it's about preparation and how you turn up to training."
The Bombers, who also delisted Jarrod Atkinson and Bachar Houli - who wants to go to Richmond - on Monday, are leaving a window open for Neagle in the NAB AFL Rookie Draft.
Hird said the powerfully built forward would continue to train with the club in the lead up to the December 7 draft in a bid to win a second chance.
"[We said], 'We'll give you an opportunity if you're prepared to work for four weeks and meet the standards the coaches and fitness staff set, and if you meet those, there's a spot on the rookie list for you, but if you don't, we need people who can meet those standards.'," he said.
"It's not that we've closed the door totally but we've set standards at the Essendon Football Club and if players can't meet them, they won't be part of our program."
The Bombers have also delisted Jason Laycock, Tyson Slattery and Michael Still, and rookies Christian Bock, Marcus Marigliani and John Williams. Ben Howlett has been promoted to the senior list.
