Problems (SPOILERS)
First of all, the entire premise is utter nonsense. There is no way in hell that his sister would be alive that long after last seen, period.
The main issue I had with Blair Witch are the two new elements introduced toward the finale - possible aliens and time travel.
The entire hook was that his sister was possibly found on video tape at the cabin. But then at the end, we're shown (in a very obvious freeze-frame) that we're not looking at Heather at all.
The biggest question here is how the hell did that happen? How could the "witch" have any sort of power over people outside of the woods? We're supposed to believe that the manufactured video was a glimpse into the future, provided by the witch?
Secondly, the "night all of the time" thing, mixed in with "it's been 5 days since we've seen you." or however many days it actually was. I liked this little addition, but it really didn't make any sense.
Lastly, the all too cliche "bright lights shining through slats of wood." If it's not aliens, what else could it possibly be?