Still happens with the latest theme.
Here are a few screenshots showing what happens: https://imgur.com/a/Wbtbg0r
(EDIT: Imgur displays the screenshots in the wrong order, so I've added the numbers.)
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Screenshot #2. Arc Dark theme after opening a Caja window: you see that the menu doesn't show everything and there's an arrow at the bottom to scroll and show more (there seems to be too much space on top so the menu appears a bit weird but it's probably a bug in the Arc theme, as I got a nice menu with the arrow when testing Manjaro).
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Screenshot #3. Still Arc Dark theme, after having right-clicked again on the trashcan: it shows the whole menu. That's where my original confusion came from, the menu first shows only part of the options, then the full ones.
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Screenshot #1. Ambiant-MATE theme when opening a new window or changing dir (same case as 1/screenshot 3): the arrow is actually there but is probably dark grey on dark grey, so it's invisible and adds to the confusion. That's why I first thought that Caja displayed an incomplete menu.
EDIT: actually, I have the same issue on Manjaro as with the Arc theme with the display of the initial menu (too much spacing on the top, separator crossing the last item), it's just that I didn't really notice when testing. So, it's possible that it's an issue with Caja that is shown by some themes more than others.