Fagan has dismissed the surface of the Lions' home ground the Gabba, or his club's training regimen, as being factors.
Two more Lions, Lincoln McCarthy and Darcy Gardiner, suffered season-ending anterior cruciate ligament (ACL) tears during last week's win against Gold Coast.
Brisbane's Keidean Coleman and recruit Tom Doedee have also torn ACLs this season, while Will Ashcroft is recovering from the same injury after being hurt in July last year.
Ashcroft, Coleman, McCarthy and Gardiner were injured during Gabba games, while Doedee was hurt at training.
"It has only been in recent times that there has been ACLs on the Gabba," Fagan told reporters on Friday.
"I don't think the surface on the Gabba has changed, so I am a little bit perplexed as to why that is the case.
Brisbane coach Chris Fagan has been baffled by the series of serious knee injuries at the club. (Darren England/AAP PHOTOS)
"I understand that people will be asking questions and trying to delve into it, but the mechanisms for each of those injuries is different.
"Our training program has been done by the same people for the last eight years and we didn't have any issues until recently and nothing has changed, so we're a little bit perplexed.
"I am suspecting that it's just bad luck, but it's incredible bad luck ... it's crazy."
Fagan said the Lions, in 13th spot with three wins and five losses ahead of Sunday's away game against Adelaide, had no choice but to move on after the double blow of losing McCarthy and Gardiner last week.
"Obviously we feel for Linc and Darcy and their families because ACLs are a major injury and they're a major interruption to your life for a fair while, so we feel for them," he said.
"But the nature of this competition is you have just got to move on quickly, unfortunately, which is what we have done this week with the blessing of those two players."
The 30-year-old McCarthy's contract expires at the end of the season, but Fagan hoped a one-year extension would be soon settled.
"We are pretty good at remaining loyal to our players, particularly when they go through a little bit of a hard time, so hopefully that will be the case," he said.
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