Question: McCoy joins Kirk for a drink, revealing a bottle he found in Chekov's locker. Firstly, what was he doing in Chekov's locker? Secondly, what's with the two of them clinking glasses with a third drink? The locker and the clinking might suggest Chekov was dead, as they might have to fill in if Anton Yelchin had died before filming was complete, but that's not what happened. Chekov is very much alive in the next scene.
Aerinah
24th Nov 2016
Star Trek Beyond (2016)
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Chosen answer: Why Bones might have been going through Chekov's locker is addressed in another answer. The third glass is not for Chekov - who, as you point out, is alive - it's in memory of Jim's dad, George Kirk, who (as Bones mentions in this scene and as shown in Star Trek 2009) died on the same day Jim was born. Because of this fact, Jim's birthday always reminds him of his dad's death, so they pour a glass, and raise a toast, in his honour every year.
Aerinah
The director reportedly said the 3rd glass was a late addition. Perhaps it can serve both purposes, the scripted intention as well as a subtle tribute. See #7 in https://www.empireonline.com/movies/features/star-trek-beyond-justin-lin-simon-pegg/.