Seems like there’s some bitrot in the middle of the file, and whatever you’re using to play back the original file just skips it and doesn’t care enough to halt playback. You might try looking for ways to restore as much of the file as possible with something like this, assuming the mkv is a unique copy that you can’t get anywhere else.
Edit: I’m also curious if this file lives on an XFS/BTRFS/ZFS filesystem. The reflink property of these filesystems may be the reason that you can copy within the same folder without it throwing an error.