Sync conflicts can happen in cloud storages (e.g., OneDrive in your case) for several reasons. Cryptomator is able to detect sync conflicts and will show you the conflicted file with a “(Conflict XYZ)” at the end.
In that case, it’s your decision what to do with it. I would check both files manually and decide which one I’d like to keep. If your conclusion is that both are identical, you can delete one copy. But that’s all in your hands how you’d like to organize your files.