Timestamps on blocks are not exact.  Protocol allows the miner to adjust the timestamp a bit in case the clock on his computer doesn't EXACTLY match someone else's clock.  Therefore when two blocks happen quickly one after the other, sometimes the earlier block can have a later timestamp.

This isn't new.  It's always happened.  Not a big deal.  Protocol is designed to handle it just fine.  The order of the blocks determines the order of the transactions no matter what the timestamp says.