Annalise was still puzzled when Mavis left her alone. She now knew what Rafael had spoken to Mavis about when he took her inside the library and he left out that it was her who told him about the gates.
It couldn't be helped that Mavis knew it was her, but it wasn't like she was trying to get Mavis fired. She was only trying to find a way out to meet with Thomas.
Now that Mavis wanted her to clean Rafael's room, she was once again unable to find a spot to train. However, if she could not leave to find Thomas tonight, since she would have to search the town for wherever he might be as it was not a day for them to meet, she would sneak off down by the river to start training again.