Shia's father was in prison for rape. He was also kicked from multiple sets when Shia was a kid for inapporpiate and threatening behaviour. Even the way he denied the abuse it was him saying "I never hit Shia in the face." He's a ceritifed piece of shit and i have no doubt he was abusive.

It just seems they've recently reconnected, so Shia started to deny it because the movie wasn't an autobiographical portrayal of his life.