How to get a dog to quit bullying an injured dog?

It sounds like the middle dog is just exhibiting innate pack behavior. In a wolf pack, it wouldn't be odd for an injured wolf to be "weeded out". An injured member of the pack can be a hindrance and a burden on the pack as a whole. Your middle dog is not being a bully or being mean-spirited - a dog wouldn't even know how to be such a thing. He/she is just acting on instinct. You just need to completely separate the two until your injured dog is healed. The middle dog must see the smaller dog as his/her strong, active self again.

These dogs seemed to have been best friends before the smaller one got into an accident and hurt her leg. Since the accident the smaller dog has been rehabbing the leg and it's getting better every day.But we're having setbacks when the 2nd largest dog of three (the largest minds her own business and doesn't have a problem with either of the 2) is bullying the smaller injured dog.The medium sized dog just mauls the small dog at any random point. Some days it can be calm, and some days we'd have to separate the two.Why is my dog picking on my injured dog?

Because the bigger dog is a bully. Keep them separated until the smaller dog is completely healed.