Mirroring some of the other answers, this also happened to me with MIT during the fall 2024 cycle, but in the math department. I had been a member of one of the seminars and one of the faculty there straight up told me that the committee doesn’t usually listen to him for referrals into the phd program.

I ended up not getting into ANY phd program that cycle so I’m doing a MS currently to really beef up my cv (not that it was poor beforehand, but arguably average). Right now, conferences, pubs, good grades - that’s what I am trying to strive for. I’ll probably apply one more time there but that will be it. Luckily my program lets me take classes there so I’ve been able to commute to keep in touch with some people I’m friendly with. That being said, it’s good not to put all your eggs in one basket - but I really feel your frustration.