On Mac in Huggle Preferences under "Shortcuts", for "main-revert-and-warn-##", the number (or N th item) is not corresponding to the correct warning. As tested today, I assigned shortcuts for "Removal of Content" and "Blanking of Page" (6 and 7) and I ended up generating warnings to users for NPOV and Reliable Sources. Huggle Version: 3.2.0 build: 3100 3.1.22-162-ga039da3
Yes. Indexing from 0. At this point the keyboard shortcuts don't even set properly though (In preferences, when I try to add or change a shortcut, nothing happens in the box - if I type the shortcut (Ctrl+X as an example) and save, CTRL+X does nothing.
I haven't come across the original issue either (I haven't specifically tried to reproduce it, but I do use custom shortcuts). I do know that certain shortcuts like Shift+D don't work at all because they're hardcoded (see T213008), but for the most part they've worked fine for me. (Big Sur, Huggle version: 3.4.10, build: 3880 3.4.10)
I also know that typing in the actual shortcut in my preferences doesn't work—I have to type out the literal string Shift+X instead of the key combination in order for it to save properly.
Additionally it doesn't seem possible to assign menu item 21 ("Vandalism") to a key shortcut. You can use Q to revert-and-warn, but the edit summary will then be default-summary instead of 02100_warning. This means for actual non-constructive edits that should be reverted with an edit summary stating as much, you have to manually click into the revert-and-warn menu.
(Enwiki has 02100_warning: "Reverted [...]: nonconstructive edits" versus default-summary: "Reverted [...] to last revision by $2", which I believe is what is used for Q.)