I do not know about the newer Marlin 39As. Mine was bought in 66.
For a fact, I know that if you run a rod threough the bore, past the chamber, the brush/patch can contact the ejector and bend it backward. On mine, there is a screw that holds the ejector assy, that, if you press the ejector tip in toward the frame, and turn that screw 1/2 turn, it will 'capture' the ejector and allow the passage of the rod/tip/jag, patch, etc.
the first year I had my 39A, I did more damage cleaning the dang thing than the following 40 years shooting it. If you just gotta clean the bore, use a bore snake...after getting the ejector out of the way.
You can visit Brownells web page, clink on the schematic pages, find the Marlin 39A, and maybe you can see what I am refering to.
The 39A malfunctioning is about as possible as your pocket change and car keys having a gravitational pull on the Andromeda Galaxy.
salty