Ok, that's helpful but we need to go through it step by step as there are so many variables.
Are you taking transaction log backups outside the log-shipping environment? If so, which folder are the log backups going to? The copy job on your secondary will only look in the log shipping folder specified in your log shipping configuration. (I've marked this path with an arrow in the screenshot I've attached.) If you take log backups that aren't stored in that folder, it will break log shipping because the copy and restore jobs won't have an unbroken chain of transaction log backups to work with.
Does that make sense? Can you check if that is happening first of all?