This is explained in the second book (and presumably the second movie)
There is a second maze, in which only girls lived. The events in both mazes were similar, both groups escaped at the same day. Also, the last person to enter the girls maze was a boy. (As Theresa entered the boys maze as last person). The Creators (of the maze) wanted to understand the difference of how The Flare attacks boys and girls, so they separated them (I can't find the quote from The Death Cure right now)
A hint to this is already given in the first trailer of the second movie, The Scorch Trials
Update (after having seen The Scorch Trials):
The creators of the "Scorch Trials" movie changed a few things compared to the second book. In the second movie, it appears that there were multiple mazes (more than two). In the scenes in the cafeteria when all gladers have dinner, we can see other boys that were not in the "original" maze (with Thomas, Newt, etc).