JG, i regret not clearly asking how much recipe product the silicon molds contain as that determines the cooking time.
Being crust-less quiche-like most Egg Bites aren't homogeneous mixtures. Depending on the ingredients you use it can be very difficult to achieve even distribution without stirring during cooking.
i use unsalted butter to grease the cooking jars and after cooking run the thin, flexible blade of a paring knife around the inside of the jars to encourage the bites out.
If the Egg Bites don't firm up satisfactorily after cooking 90 minutes you might consider reducing the amount of liquid ingredients other than eggs. Also, use the freshest eggs you can source, Some ingredients such as ham, eggplant, zucchini, tomatoes and onions can add significant water to the mixture as they cook. Sauté and cool moist ingredients before adding them to your egg mixture. Cottage cheese needs to be drained in a coffee filter lined strainer before use. If your recipe requires lemon just use finely grated zest, and only a little.
If all else fails, try blending or whipping a little corn starch into the egg mixture to tighten it as it cooks. Start with a scant 1/4 tsp. to 4 eggs, that should do it.
And lastly, maintain a detailed record for each batch so you can achieve repeatable perfection once it's attained.