Virgil likes to scratch at his neck. His neck is covered in red scratch marks. He wears his hoodies to help hide his scratch marks. Logan knows about this, and actively tries to stop him from doing it. Virgil once went through a pain withdrawal for three weeks. In that amount of time, he was very irrational and irratible. His presence in Thomas's mind in that amount of time was basically non-existent. After those three weeks, he continued scratching at his neck. He kept doing it.
Nobody wants to have an angry Virgil, so they leave him alone about it.