I hadn't gotten to blue (Science 3) production, but it decided to keep sticking me on a recipe (I don't know why it was created thusly) with two ingredients, one Science 1 pot, and one Science 3 pot. Since I could not yet produce science 3 pots, if I walked away (I sometimes let my game run unattended, thanks to you and this mod you keep running !Thanks!) all research comes to a halt when it hits this. Would you be so kind as to make it check to prevent this from happening? I'd appreciate it.

I'm guessing this research recipe is added by another mod. Auto Research currently doesn't know which science packs are more difficult to create, it only sees how many types of science packs a research recipe requires, and then chooses to research whatever requires the fewest types of science packs. For example, with just the base game AR will research everything that requires just red science before researching stuff that requires red and green. When all red and green research is done it'll start with red, green and blue research. This works well with just the base game as all research that requires blue science packs also requires red and green. However, when you have a mod that adds research that require red and blue, this will be considered equal to red and green. AR doesn't know that blue science packs is more difficult than green science packs.
This is sort of not an easy problem to solve as some mods adds new ingredients to research (such as Bob's mods) and I thus need a generic approach to selecting research. I don't think I'll do any modifications to AR this time, but I'm keeping it in mind for Factorio 0.15 which is likely going to greatly affect this mod.

I have the same issues,whilst running the research revolution mod, adding 0.15 science. A quick fix is to add science packs you want to research to the standard science pack list and remove the ones you dont want. In the long run a nice fix could be to detect the available types of science packs and just have checkboxes to enable or disable packs. Alternatively you would have to add them in a config file yourself. So remove the non-standard ingredients checkbox, but keep the function. Use this function to enable or disable specific packs.