Star Trek Beyond: 25 Easter Eggs, References & In-Jokes

Early on in the film when Kirk is talking with Commodore Paris and volunteers to lead the mission to save the stranded ship beyond the nebula, she briefly mentions that there's only one ship capable of outstripping the Enterprise, which is still in production.

Later, after the Enterprise is (once more) symbolically destroyed by Krall's ships (echoing the way it was in The Search For Spock) and Kirk uses the Franklin to get home, we get to see the ship. It's the Enterprise-A - the same ship that Kirk takes control of during The Voyage Home.