When Kirk asks Scotty to travel to a set of coordinates given by Khan, he finds the USS Vengeance and flies in alongside other smaller ships.
How did he not get caught?
His ship is surely different than the other ships. And as USS Vengeance was supposedly, at the time, the most advanced starfleet ship, wasn't there some protocol to make sure each of the smaller ships leaving/entering would be registered?
According to the film's official novelisation he used the planet's magnetic interference to disguise his approach, then simply hid his shuttle in amongst a small convoy bringing parts and technical crew to the Death Star USS Vengeance. The sheer volume of ships, confusion over their numbers and call-signs and a general air of complacency was sufficient to get him into the ship's vicinity.
Wait a minute, he told himself. They weren’t talking to me. Whoever they were. In fact, from the gist of what he had overheard, “they” weren’t even aware of his presence. Not surprising. This close in to the gas giant’s powerful magnetosphere, there was all kinds of distortion on the spectrum, and plenty of upper hybrid resonance instability. Communicating inside the Io plasma torus was difficult enough, and scanning more so. Subject to such powerful external influences, instruments didn’t behave the way engineers wanted them to.
then
As each of the arriving craft gave their name and detailed their cargo, it occurred to Scott that he might just possibly be able to lose himself in the confusion. Bringing himself down and around, he slipped easily into the cargo fleet’s scattered formation. There was plenty of room for Scott to maneuver among the other shuttlecraft. No one questioned his presence. After all, what would another single, small shuttlecraft be doing in Io’s vicinity? All current scientific work was performed by automated spacecraft and instrumentation.
Precisely how he got on board isn't described, but it's noted that he recognises the ship as Federation-designed so presumably he'd have knowledge of how to use the various emergency entrances and exits without setting off alarms.
