May I ask how you play it? I have problems with both the R12 and R13 of the Mega65 versions. One can't save, the other freezes and crashes when typing in commands :(
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You saw this? https://8bitgames.itch.io/hibernated1/devlog/416076/bugfix-for-mega65
So if you downloaded R13 on the original R13 release date, it still had an issue. You should be fine when downloading it again now.
I do have a MEGA65 myself and the game runs fine on it. Make sure that you run the latest MEGA65 core and Kernal.
I have a brand new Mega65 from the latest batch with ROM V920395 and downloaded the latest R13 archive two times. But there seems to be something wrong with the .d81 image.
My Mega65 seems to mount the image, but when I try to copy it to an actual 3.5" disk, the Floppy/d81 Imager V1.7 from Intro disk #3 can't read the image (in contrary to all other images on the sd card).
When I start the game I can hit Return and get an answer, but when I enter any word it just freezes.
I've updated the disk to use the modern Ozmoo interpreter instead, as I am doing with Ghosts. Feel free to download the archive once again and test if it works now on your MEGA65.
I am guessing something must have changed in the MEGA65. The old image was created by Deft, one of the MEGA65 admins. There is no chance it did not work and it definitely worked on our machines when we tested it.
PS: There is a slight chance that the error you are encountering, especially when trying to copy to a real floppy is related to your SD card being fragmented. That has nothing to do with the disk image itself but with the way you put files on the SD card. Regarding making a copy of it onto a real floppy, please refer to the MEGA65 Discord, as that has nothing to do with the disk image per se :)