The other was a military salute. They passed some regiment who saluted them, Wills in turn as a military officer saluted back though as a royal he could have just lifted his hand or nodded his head, Kate bowed her head to acknowledge the honor.
If you notice when people bow or curtsey to the Queen, she slightly bows her head in acknowlegment, when you watched Kate she was watching William out of the corner of her eye, when he saluted she bowed her head, when he dropped the salute she lifted her head.
The announcer talked how on the way to the church Kate recieved no salutes but on the way back she did as she is now a Royal and entitled to the honor from the military.