Bowyer received a yellow card from referee Lee Mason after a late lunge at Gibson who was starting his first Barclays Premier League game since April.
Ferguson felt Bowyer, who is 34 next week, should have been given his marching orders and he took advantage of staying on the pitch by scoring a last-gasp equaliser.
The United chief fumed: "The Bowyer tackle in the first half, I thought it was a red card. He's gone over the top of the ball.
"Bowyer has been given a yellow card so nothing can be done about it (retrospectively). But it's a dangerous tackle."