Hi Hugo
Can you please report the specific GoCD version you are using and the full stack trace of the error from the server logs?
It's probably necessary to know the specific operation that failed and the version you are using to know what limits might be applying.
It may also help to know what git object type that is with git cat-file -t 2506f3dcaf16646bf525968cd53bd023872d72c0 (will have to run inside the config folder on your GoCD server).
There are a few other similar issues reported against tools that use JGit, but I didn't come to any specific conclusions about what caused them, so probably need more specific details here.
-Chad