Private information out of the club was posted online ahead of the Lions' 64-point mauling of the Bombers on Saturday.
Photos that listed the strengths and weaknesses of Essendon's players were shared in a Bomber supporter group on Facebook.
Former Essendon captain Zach Merrett was described as "selfish", while maligned defender Ben McKay had "low confidence" written about him.
"Somebody illegally took photos of information that was on a whiteboard and then decided to make a hero of themselves and put it out in the public domain," Fagan said.
"I reckon it's a little unfair when it's your workplace and it's what you do every day ... we've been doing it for nine years ... writing the strengths and vulnerabilities of opposition players up on a whiteboard.
"That man was there with his children, using our facility, and he decides to do that because he's an Essendon supporter and be a hero.Â
"I think that's really disappointing."
Former Lions defender Jaxon Prior's only strength was listed as 'Bronte', the name of his long-term partner.
"I spoke to Jaxon out on the field after the game, as did a lot of our players, and had a bit of a laugh and a joke together," Fagan said.
He admitted the incident made him think twice about allowing external people to access facilities at the club at their Brighton Homes Arena headquarters.
The dual premiership coach said he learned the exercise of listing the opposition's strengths and weaknesses from former Wallabies mentor Eddie Jones.
"We go out of our way to bring the community into our football club and use our facilities," Fagan said.
"For someone to do that, it's really disappointing, and it makes you feel like not bringing the community in and just keeping it exclusive as an elite performance centre.
"But we'll keep bringing the community in, because we're a good footy club, and that's how we go about things."
The usually reserved Brisbane star defender Harris Andrews was also furious about the incident when speaking after Saturday's win.
Essendon coach Brad Scott was unfazed by the incident, saying it was an issue for the Lions to deal with.
"Brisbane have done that (listing strengths and weaknesses) for years, so that's nothing new," Scott said.
"I wouldn't want that coming out of our building."
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