On the logic front, there is the question of why didn’t Kirk have the shields up approaching the unknown planet? They had to have been up getting through the rock-crushing debris fields of the nebula, so why turn them off?
On the tech front, the first appearance of Jaylah’s hologram technology is confusing. She uses a portable device to create hologrammatic, independently acting duplicates of herself, which, it seemed actually hit some of the bad guys. This presumably alien tech is superior to the Next Gen holodeck technology since it is portable and programmable on the fly. (Projection: Jaylah, who’s been accepted for Star Fleet Academy, finds that Federation sim tech is less sophisticated than hers, goes into business supplying what becomes Holodeck/emergency medical hologram equipment, and retires very rich--).
The design of Starbase Yorktown is wondrous, but nonsensical in a number of ways. Why should a starship be able to “drive” all the way to the center of the base when there’s no reason for it to, and many why it shouldn’t? The master ventilator node is located at the physical center of the spherical construct, but only accessible by a series of perilous ladders. The answer to that one, is so that there can be an exciting fight scene, but that’s pretty much the rationale for the whole film.
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