Extra liquid at the bottom of cooked shepherd's pie can come from a variety of sources. One of the main sources is the ratio of meat to broth. If you are using a type of meat that doesn't soak up the broth well as it cooks, you'll have extra water. If you're using frozen vegetables that aren't thawed and dried, some of the frozen ice around the veggies - even a teeny tiny amount - will melt and add liquid to the dish. If you have extra liquid, simply lift the pot and very carefully pour the excess liquid into the sink.