First time when I built a couple of apostles I wanted to attack the french missionaries. But I couldn't. Is it because I am not the founder of that religion? Or is it because I am not at war with france? Or something else?
You don't need to be at war with someone or to be the founder of your religion to engage in theological combat, but you cannot attack religious units of the same religion. Are the french missionaries of the same religion as your apostles? That would be my guess.
Side Note: Only Apostles and Inquisitors can engage theological combat themselves, missionaries can only defend. (Just relevant info to the title, not your question)