Corrected entry: When Kirk et al are seen walking through the Enterprise shuttlebay, the shuttles are showing the registry of NCC1701A. The Enterprise's registry code, as seen throughout the film on the ship's hull, has no "A" suffix.
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Correction: The only shot of the Enterprise shuttlebay interior is the one through the main shuttlebay doors when the ships first land aboard the Enterprise. No one is ever seen walking through the Enterprise shuttlebay. You might be thinking of the shuttlebay in Starfleet headquarters., which includes multiple ships, some of which might have an A-designation. The two Enterprise shuttles I noted show no such A-registry.