Checkout confilict with no changes

I am facing a rather strange issue, it maybe that i am doing something wrong.

I am looping over all branches, i then locate certain files, i then read something from the files and then move on. But i can't move on because i get conflicts when i switch, and this is where it gets strange, because i do not change anything at anytime in this process, so why is it telling me that there is a conflict??

One thing i notices is that, when submodules is behind, don't know if that has something to do with it

var repo = new Repository("path to repo"); foreach (var branch in repo.Branches) { repo.Checkout(branch); dosomthing(branch); }

Start by reproducing the loop around Repository.Checkout(branch), including the reported case where a submodule is behind. Inspect the checkout behavior and captured repository state when no files are changed. Done means identifying the cause of the conflict and adding a regression test or a precise fix path for this scenario.