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

Eventually, it's revealed that Jaylah's "house" is in fact an abandoned Federation vessel - the USS Franklin, which she has hidden using deflector technology (despite the fact that it turns out it's Krall's ship and he's apparently just forgotten where he parked).

The familiarity of the ship shouldn't be surprising: the bridge is very much reminiscent of the Original Series design, plus the ship itself looks extremely similar to the Enterprise NX-01 seen in Star Trek: Enterprise. It also has the registry number NX-326 confirming it was in service during the 22nd century.

Further than that, the fact that Krall reveals he fought the Xindi seems to suggest he may even have been a crew-member of the NX-01 at some point.