The potions regiment Susan and Theo had put her on was intense and was, at this point, mostly guesswork. They knew she was likely experiencing some severe nerve pain, as her diagnostic scans consistently revealed angry, pulsing bright blue indicators. The potion designed to alleviate nerve pain was a work in progress, something that Theo hadn't had much time to fiddle with before administering it to her was a necessity. It was Susan's opinion that the screaming was a result of the pain breaking through the potions efficacy and whatever brain-imposed deep sleep Hermione was currently under. And so they (well, Theo, mostly) brewed and researched and made changes to a bog standard pain potion in an effort to find something that worked. So far, no luck.