I have since upgraded from 20.04.4 to 22.04 and can see the same bug.
Mutiny layout with Plank dock shows a second icon for Caja when:
1- click on trash icon in dock (when no other Caja window is open)
2- or, plug in an external drive (again, when no other Caja window is open)

In both situations, a second Caja icon appears at the bottom of the app list in 
the dock.  Subsequent "new window" requests from the Caja menu add to that 
second icon.
Clicking on the first, pinned Caja icon in the dock opens a new window, again 
linked to the second icon.
Clicking second icon works as expected, switching to Caja / minimising all Caja 
windows / bringing them back

screenshot attached of external drive with both Caja icons.

** Attachment added: "screenshot-with-second-caja.png"
   
https://bugs.launchpad.net/ubuntu-mate/+bug/1970062/+attachment/5591129/+files/screenshot-with-second-caja.png

** Summary changed:

- 22.04 MATE Mutiny dock bug with Caja and trashcan
+ 22.04 MATE Mutiny dock bug with Caja - second icon shown

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https://bugs.launchpad.net/bugs/1970062

Title:
  22.04 MATE Mutiny dock bug with Caja - second icon shown

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