Same issue here.
git checkout and git merge of a remote branch to local through SSH is failing with:
Downloading <object> (13 KB)
Error downloading object: <object> (): Smudge error: Error downloading <object> (<object>): batch request: unexpected end of JSON input
Errors logged to ----
Use `git lfs logs last` to view the log.
error: external filter 'git-lfs filter-process' failed
fatal: <object>: smudge filter lfs failed
Switching to https does resolve the issue for now. This is not a solution, SSH needs to work.