“a San Francisco startup” /ə ˌsæn frənˈsɪskoʊ ˈstɑɹtˌʌp/
  vs
  “an SF startup” /ən ˌɛsˈɛf ˈstɑɹtˌʌp/

i.e. you have to mentally pronounce the phrase before choosing which form of the indefinite article to write