The statement "top two finish in each individual event with an OQT" wasn't true in 2012 and it isn't true now! In 2012 it was sufficient for the winner of the race to achieve the OQT. For the second placed swimmer to gain selection they had to achieve an OQT and that time had to be faster than the time of the 16th placed athlete in the LC rankings.
See http://www.swimming.org/assets/uploads/library/2012_Olympic_Games_Pool_Selection_Policy_-_Final_Amended_19_Dec_11.pdf
In particular see clause 1.4.2 - "The 2nd place in each individual event will be filled by the 2nd fastest 'available' swimmer in the final of that event on condition that they have achieved the world long course ranked Top 16 (2 per nation) time as set out in Table 1 in the 'trials' final of the said event. Such a nomination will be subject to clause 3.2"
Most, if not all, of the target times for the second placed swimmers were faster than the OQT. As an example Molly Renshaw finished second in the 200m breaststroke at the 2012 trials in an OQT but failed to secure selection after failing to achieve the Top 16 time. I've not finished analysing the 2016 policy yet but it appears that it may be even more complex than 2012 this time.