At the beginning of S3:E1 Pike asks Uhura to repeat April's orders that were originally given in the final moments of S2:E10. Uhura reiterates the orders: "rendezvous with the fleet", Pike says "... but he didn't say 'immediately'" and uses this as a loophole to proceeds with his own plans - but in S2:E10 when Uhura conveys April's orders they do in fact include "immediately".
If the Enterprise was inside the destroyer's shields it could have just beamed the missing crew and colonists back aboard at that time.
Admiral April says that "Apart from your reckless dogfight, these attacks do not involve the Federation". This is nonsense as at least two Federation ships have been destroyed by this point and another attacked while on it's side of the Gorn's demarcation line.
The tracking plan involves modifying a torpedo with Wokite but then they never do this, they just shoot normal torpedoes at the enemy. They don't even convert them to "dud"s.
Uhura states "The Gorn must not use optical data. They've evolved, so they must rely on biometrics, heat and EM signatures."
Heat, optical both types of EM so this just nonsense.