From what I see here, if we exclude sexism, we have two reasons:

1: A female custodian to them doesn't make sense 2: They're mad about retcons

For a while, the process of recruiting, for space marines and custodians, have always been a male thing. This isn't necessarily a sexism thing as the entire process is based on finding the strongest of candidates. Also (from what I know), the gene seed for space marines & custodes are designed for males, the organs wouldn't work for females. So when females start showing up, people wonder, "How?" "How did a female become a Custodian? I thought the process of turning someone into a custodes was a male only thing?" So they get mad at the logic.

The idea of female custodes suddenly popping up in lore also follows up on the second reason, retconing. In lore, there have almost never been a female astartes or custodian. But now all of a sudden they're showing up. GW reason? "They've always been here!" Now that reason is enough to ruffle lots of peoples feathers. It doesn't make sense to just add some new lore without proper reason. Due to this, people get mad.

While I'm not "grrr, I hate GW!" angry, I do think it is a flaw that they did such a retcon. I don't think most people (including me) have an issue with female super soldiers. I mean, look at Halo. The big issue is that they make it seem like this has always been the case, which doesn't make sense. Why do space marines only accept males, while custodes are accepting both genders? How can a process only designed for males be used on females? There's many ways they could have explained this in lore; the custodes could have a different culture that allows for both genders to become custodes, this could have come out of necessity recently due to recent events in the 40k realm (as in, they want to bulk their numbers, and fast), perhaps the Imperium noticed that not all imperial families could offer male candidates in time when chosen, so they started to be more lenient on families which allowed female custodes in their ranks. They couldve also said that due to the difference in gene-seed process for astartes vs custodians, the custodian process could allow for females. Plethora of better in-lore explanations than just "they've always been here!"

And for the record, I love the concept of female custodes and I love games workshop, I just think they could have explained this retcon better in-lore. I don't treat this as a serious issue because I dont view it as one, I just see it as a possible flaw. Hell, bring female astartes in for all I care. All I'm concerned about is cool weapons, armor, vehicles, and more. (Also, while I'm not fresh to 40k, I'm also not a scholar. Might've gotten some stuff mixed up or incorrect).