(Not a Teacher)
Sometimes "at" and "in" are interchangeable, sometimes they aren't. For both of your sentences, I would use "at"
"I am studying at UCLA."
-- "In" just doesn't sound quite right here. No particular rule, I think, that's just how it's expressed.
"I'll wait for you at the movie theater."
-- You could use "in" here, but it would imply that you will be waiting inside the theater. "At" is non-specific. It simply means that you will be hanging out somewhere in the vicinity of the theater.
Student or Learner