If he had said something like nous pouvons nous retrouver… that would seem like confirmation was needed, but his use of the future seems pretty clear to me: I would have felt as you did. So in retrospect, all I can suggest is responding with something like D’accord, à jeudi (or whatever).

If you want to make sure you confirm an appointment and tell you’ll be there, just express it clearly, e.g.:

Merci de votre proposition de rendez-vous. L’heure me convient. Je vous confirme donc ma présence le xxx à xxx heures.

(heure) est bon pour moi might indeed be misunderstood as you just tell an unidiomatic way the time is good for you without explicitly confirming you’ll be there. It is however unclear why “Nous nous retrouverons à xxx” was answered if your party wasn’t understanding the appointment to be confirmed.

To be honest, their answer is not that unclear (at least to me).

But since you are a little bit worried/unsure of your answer especially that you do not show us the previous conversation with them, then put in your mind that there is nothing bad in confirming them again that you agree with the appointment. Thus, you can answer them something like this:

Je vous en remercie et je tiens à vous confirmer ma disposition pour
le rendez-vous que vous venez de me fixer pour le jour/mois prochain
à heures:minutes

Merci, je serais là à (temps).

Je serai là at time (futur) is correct but not really used in a written communication.