What had Todd really done to Bud before his mother came into the room in Bud, Not Buddy?
Todd had provoked a fight with Bud, and before his mother came into the room, had given the smaller boy a sound trouncing.
On his first night at the Amos' house, Bud awakens from a sound sleep to find Todd sitting on his chest, trying to stick a pencil up his nose. When Todd goads him, Bud swings "as hard as (he can) at Todd's big balloon head" and ends up smacking him hard once with an open hand on the jaw. In the fight that ensues, Bud discovers that "even though Todd (is) a puffy, rich old mama's boy who (wears) a robe and slippers he could hit like a mule". Bud is taking a beating when Mrs. Amos walks into the room.
Todd's demeanor changes completely when his mother walks in. He fakes an asthma attack and shows Mrs. Amos his jaw where there is "a perfect print in the shape of (Bud's) hand welted up on Todd's blubbery cheek". Playing the role of the victim, Todd lies and tells his mother that he had only gone to wake Bud up to make sure he used the restroom so that he wouldn't wet the bed like the other foster children they have had did, and that for no reason at all, Bud had attacked him. Without giving Bud a chance to tell his side of the story, Mrs. Amos banishes him to a small shed outside, where he will wait until the social services people come to take him away in the morning. She also makes Bud apologize to her precious son Todd, under the threat of giving him "the strapping of (his) life" (Chapter 2).
In the children's novel, "Bud, Not Buddy," Bud was removed from a Flint, Michigian orphanage, and placed in the home of a foster family. The Amos family took Bud home but Bud could tell early that there was going to be trouble. Todd, the Amos' son resented Bud and harassed him from the start. In the section you are asking about, Todd had awakened Bud by shoving a Ticonderoga pencil up his nose.
When Bud awoke with the feeling that he was smothering he slapped Todd. Once slapped, Todd began to beat the smaller Bud. Todd's mother came into the room and she listened to Todd cry and complain about how Bud attacked him. She saw the slap marks across his face and decided Bud must go back to the Orphanage.