No, not yet, but the new film was only announced in February 2012 (the release is currently scheduled for June 2014) so there is a long way to go yet.

However, there has been at least one injury on the set of Transformers 3: Dark of the Moon. This was released in 2011, but the court case on the injury has only finished very recently. The accident happened to an extra named Gabriella Cedillo. She was driving a car for the background to an action sequence, when a cable from a stunt car hit her car and smashed through the windscreen. She was hit on the head and suffered brain damage.

Cedrillo sued Paramount and Dreamworks studios for damages and medical expenses, and she was finally awarded a settlement of $18.5 million even though an earlier investigation had not found the company to be in breach of any safety laws.