Infections are easy to get when the animal gets stressed, like when it gets moved. This is especially true for young animals that have just een weaned. Stress lowers immune function and makes them more susceptible to things.
They may be getting better now and have a better appetite for hay, but it's been my experience that cows don't want junky hay. It doesn't have the nutrients that growing calves need. It doesn't smell or taste as good as high quality hay. You can mix the two together and that may work, but make sure the junky hay doesn't have mold on it. That can cause problems. Also, if it's very dusty, that can be a problem.