I bottle my own hot sauces and it just seems that I can't find a consistency when it comes to the sauce separating. I'm hoping that getting the correct method/amounts will help.
Generally speaking, the cause of such separation is either too much water in the sauce, or two non-miscible substances (like oil and water) that are not forming a true suspension. Commercial sauce manufacturers use a stabilizer like xanthan gum, which is not commonly available to amateur saucemakers. If you are moving into the professional arena, I suggest finding a co-packer to bottle for you.