This is a new problem, I guess has little to do with submodules.
I'm guessing that the patch you create does not "fit" into the repository
where you are trying to apply it, maybe because other changes have occurred
in the mean time. I can't really say any more without seeing the entire
error message, the patches you are trying to apply, and the repository you
are trying to patch.
If you're unable to share the details, you just have to keep reading
(google "git format patch"), and trying it out (I don't have so much
experience with patches myself either).
Try creating a little testing git repo with a few commits, which you clone
locally, and then try patching changes from one to another, make some
conflicts, see what happens, and so on. Here's a similar
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