Cauliflower cheese can go watery if the cauliflower is overcooked. Overcooked cauliflower releases water, which will seep into the rest of the dish. So even if your sauce was thick when it went in the oven, if its in there too long, the water from the cauliflower will cause it to go watery. I would advise to not bake for longer than 20-25 minutes. If by this point its not quite brown enough on top, remove from the oven and place under the grill on high for 1-2 minutes.