It's because they did a gender test on those athletes. They aren't trans, they are DSD or intersex. This boxer identifies as a woman and has been socialized as a woman, but she is biologically male (xy) because she has internal testes. This means she produces testosterone at male levels and has gone through male puberty. Testosterone is the driving force behind athletic performance.
It's the same issue that Caster Semenya encountered. Unfortunate for the athlete to deal with that level of scrutiny but if we look at it at the scientific level, it is fair to say that allowing this athlete to compete is unfair for biological women (xx) because even women who produce higher level testosterone on average, do not come close to producing at the same levels as men.
There's a lot of misinformation going around with people saying things like oh, she's just producing higher levels of testosterone. While true, they aren't saying it's because she's gone through male puberty.
And yes, it appears she has lost a number of times before but that really isn't the discussion. The discussion is whether or not these athletes have an unfair advantage over biological female competitiors. We also need to remember that categorize athletics for a reason. If there was no female category, women would never win. It's the same reason why they are weight classes in boxing and why we events like the Paralympics.
Really this a failing on the IOC for allowing this to happen again. Canadian Melissa Bishop lost in 2016 to three DSD competitors.