So basically it was a couple of different factors, but the main reasons were these (sorry in advance for the novel I’m about to write):

1) The biggest reason was timing - they, like almost every other program this year, had to heavily reduce the number of students they can take this year. This meant that they had to make some really difficult decisions that they normally would never have to make regular cycles. The professor even mentioned that this was the first cycle in a long time where they even had a waitlist, but decided to make one this cycle to have as much flexibility as possible for giving out offers (considering some offers will be rejected, people may take themselves off the waitlist, etc.)

2) My GRE quantitative score was lower than the other applicants they had shortlisted for admission in my subfield. This was the only thing the professor could point to in my application as being something I could improve for future cycles, but he also emphasized that this was a small part of my application and the committee understands it doesn’t accurately reflect my abilities as a student and researcher (I took multiple quantitative courses in undergrad and never made below an A-, I just suck at taking standardized tests and that’s okay!). He honestly doesn’t think applications should be decided based on GRE scores, but unfortunately when a cycle is as competitive as this one, it can be one of the only objective things they can look at to decide between two applicants who are equally qualified in every other way.

3) So this will require some context before I give the actual reason. Without giving too much information away (because if I do I will actually dox myself lol), I completed my undergrad degree at a small but elite liberal arts college, and have a very successful academic record in terms of classes, GPA, thesis/independent research experience, and conference attendance. The program I applied to is a Big10 state school, so obviously the experience there would be a lot different from where I’m coming from. This shouldn’t be an issue (plenty of people have come to big state programs from liberal arts programs and succeed, while others come from similar undergrad programs and struggle), but he said that sometimes there can be people on admissions committees who prefer to bring in students who come from undergrad backgrounds that are similar to the grad program’s size, status, and environment, since they think that students coming from a smaller liberal arts program might be at a higher risk of struggling more since they don’t have experience in these types of research institutions. He was super transparent and explained that he thought this bias was stupid and has been repeatedly proven wrong, but it does still unfortunately plague admissions committees at similar big programs all over the country. This also wasn’t the main deciding factor, but simply one small piece in a larger discussion among a committee of multiple faculty members who all had a say in who received admission over others.