Why does it say that Protozoa is not a subkingdom and that Protista doesn't exist at all in the taxonomic tree thing on INaturalist?

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Literally why??? Also, another thing I noticed is that domain is also excluded.

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Higher level taxonomy has been in flux for a few decades. Most recently, DNA evidence has really changed our view of higher level relationships. Here’s some information about that in a previous post: https://forum.inaturalist.org/t/why-are-ciliates-chromista-i-thought-they-were-protozoa/18129/5

Most people studying relationships at this higher level don’t bother with the standard taxonomic hierarchies (subkingdoms, phyla) and just name major clades. Here’s an example: https://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(19)30257-5

And a 2001 article about the “protozoa”: https://bioone.org/journals/the-american-biology-teacher/volume-63/issue-7/0002-7685(2001)063[0483:TPAKBD]2.0.CO;2/The-Protozoa-A-Kingdom-By-Default/10.1662/0002-7685(2001)063[0483:TPAKBD]2.0.CO;2.pdf?casa_token=xxQuYP49D6oAAAAA:C6H5lNJFrEezqCr8qg57rywK3sIB2tNPn8zr3wTEqnK09vkaWnIDMI3d-76ZOxhRtKQ1CyNNJg

Both protista and protozoa have long been recognized as “catch all” groups rather than evolutionary groups with shared common ancestors. iNat taxonomy sort of does the best it can given the current state of flux.

It’s my understanding that iNat follows the taxon framework of the Catalog of Life:
https://www.catalogueoflife.org/

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“Protozoa” and “Protista”, as @pfau_tarleton said, are catch-all names for all single-celled eukaryotes that are not photosynthetic. It is a grouping that has no biological meaning as it encompasses organisms from all over the eukaryote tree of life, and frankly isn’t very useful either.
The names haven’t been used by actual biologists for decades now, and thankfully, iNat somewhat follows the scientific developments in terms of taxonomy

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“Algae” is a similar catch-all bin that is a polyphyletic grouping of all sorts of organisms, even including some prokaryotes (cyanobacteria). As far as I know, Protista included eukaryotic algae, at least our old botany text did. Our botany textbook finally did away with “Kingdom Protista” for good some time between the 2005 and 2013 editions.

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My wife made this sign that hangs in our kitchen as a reminder of just what a mess “protista” is as a kingdom:
https://ibb.co/YP8Dv1N
I’d say the reason “Protista doesn’t exist at all in the taxonomic tree thing on iNaturalist” is because Protista doesn’t exist at all as a category in most modern taxonomy.

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So why are angiosperms divided into monocots and dicots, with Amborella and magnoliids in dicots, when we’ve known for over twenty years that they don’t belong there?

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As was stated earlier, Inat’s base database follows the catalogue of life. Now, a curator can go in and add or delete a few species names when need be to keep up to date, but the overall framework is kept the same. Otherwise, we would consistently be seeing major taxa being flung all over the place which honestly does more harm than good on a website like this.

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See ongoing discussion on this flag: https://www.inaturalist.org/flags/240790

Mainly it’s an issue of system capacity to implement changes at deep nodes involving many millions of observations.

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There’s a list and discussion of other base-level non-monophyletic taxa like this here: List of paraphyletic groups in iNat’s Taxonomy
Similar reasons for all of them.

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That is true not just of “major” taxa.