In my case with Ubuntu 14.04.3 and Apache 2.4.7, the problem was that I copied site1.conf to make site2.conf available, and by copying, something happend and I could not a2ensite site2.conf with the error described in thread.
The solution for me, was to rename site2.conf to site2 and then again rename site2 to site2.conf. After that I was able to a2ensite site2.conf.