There were two scenes where Kirk talks to Spock about tricking V’ger and then makes a fake speech to his crew while the woman probe takes a tour of Engineering. The probe makes an insult about Scotty’s engines and he gets pissed.

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This is a clip where one of the Security guards gets zapped by the space probe that enters the Bridge. It’s the black guy that gets it, you’ll see the remaining guard walk of the bridge sad that his buddy is gone.

It was deleted because of a statement about “Only two, report them as missing.” When there are three people missing on the ship. this one is mentioned by Bob Wise.