There's also some dialogue on the tape extract playback that Lt. Shaw plays as evidence for the court:
Uhura: Call from the pod, sir.
Kirk: Tie in.
Finney: Finney here, Captain. Ion readings in progress.
Kirk: Make it fast, Ben-- I may have to go to Red Alert.
So evidently, the pod wasn't simply being readied
to take readings; ion readings were actually in progress.