Yes 2016 is the 50th year since Star Trek debuted, but the 'first anniversary' of something is one year after the initial occurrence, so the first anniversary of Star Trek would have been one year after its debut, which would have been in 1967. Counting up 50 anniversaries from the first one in 1967 gives us 2017. This means that 2016 is the 50th year of Star Trek's existence, but only the 49th anniversary.
Think of it as birthdays. Say you were born on September 8, 1966. You turn one year old on September 8, 1967, or the "first anniversary" of your birth. When you turn 50 on September 8, 1966, it will also mark the "50th anniversary" of your birth. Counting from 1967 to 2016 is 50, not 49 (jot it down or make a quick spreadsheet).
If the 2260s Prime Universe does appear in STIII, then let's not have any CGI hocus pocus or enhanced TOS clips. Let's have replica TOS sets and let Pine, Quinto, and the others play the characters in both universes. Talk about heads exploding.