Maybe it's because he doesnt have enough rep to comment
No. You can always comment on answers to your own question. What happens quite often is that (for example after migrations), the OP loses ownership of the question (e.g. by losing their cookie) and they can't comment anymore.
In this case though, the OP probably doesn't understand how comments work.
How do we deal with this - in addition to rejecting the edit ?
If the OP failed to comment, you can try to paraphrase their suggested edit as a comment to the answer. This way the information isn't lost, and you've helped both the person answering (because they know what's missing and how to update), and the OP (because their message was somehow delivered).
Has anyone else come across this, should I just add a comment to OP to not do this?
Seen that plenty of times, but rather in conjunction with a migration (see above). In these cases, I'll tell the users to log in to the site to gain control of their question again.
If the OP could have theoretically added a comment, the "invalid edit" reject reason should actually tell them why this doesn't work. But as these users somehow didn't get the way the system works in the first place, they probably won't understand the reject reason as well.
Just tell them not to do this and give them a quick introduction about how edits and comments are supposed to be used and that the two shouldn't be mixed up.