I wanted to back up the SD card that I use for homebrew on my 3ds xl, so I inserted it in my laptop (linux) and first I tried to dd it to an .img file but I got io errors so I mounted it and could navigate it without any problems. So I started copying all the files from the mountpoint to a separate folder which also gave me io errors on a lot of my games, almost all .nds, .3ds and a lot of files from ctgp-7, but I've never had a problem on the 3ds itself so I'm wondering what the issue is and if there is a solution I'm not aware of.
in the attached image, you see the difference between the folder I copied and the original
in the attached image, you see the difference between the folder I copied and the original