I just wanted to suggest that we file a bug for this on GitHub, because this was something that also immediately confused me when I started to evaluate Zammad. Turns out there is already one: "Reply" action in UI unclear · Issue #372 · zammad/zammad · GitHub
@MrGeneration would it be possible to unlock the issue again so we can upvote it? GitHub won’t allow voting on locked issues 
@antweb Have you considered to do in-house training for your agents and explaining the problem to them? That is what I’ve done, though I can’t say yet how well it’ll work, as we’ve haven’t started using Zammad yet ^^
An easy workaround would be to edit the translation (assuming you’re using a non-English locale). Ensure that you’ve chosen a non-English locale (e.g. German) in your profile, and then go to Admin → System → Translations, and search for “Enter Answer or”, and change the translation to something like “Interne Notiz eingeben oder”. The UI will then say “Interne Notiz eingeben oder Dateien wählen”, which hopefully should make it clearer to your agents that that field is not the proper way to reply.