Mostly it comes down to a tradeoff between taxonomy and the way people use the site. When Pisces was broken up a bunch of IDs of sharks and rays ended up as Vertebrates when people tried to ID them as Fish. It’s still an issue for anybody who is a casual naturalist looking for an identification without detailed knowledge of formal taxonomy. There are other examples.
Topics like this: https://forum.inaturalist.org/t/list-of-paraphyletic-groups-in-inats-taxonomy/19456/9
have discussed this.
As a learning tool for ordinary folks with an interest in nature it’s important that iNat doesn’t assume expert knowledge of anything much. Part of the learning should be developing an understanding of how groups are related, which groups aren’t real and which relationships are mysterious (or at least I think it should be) but a person coming in as a newbie needs to be able to navigate the site.