Ben was a Maze Runner who attacked Thomas after Ben was stung by a Griever. The boys seem shocked that Ben was stung "during the day." If he was stung IN the maze then what was he doing back all ready; it was still early in the day. Why didn't anyone notice his incredibly early return. If he had been stung the day before then the reaction took time (which didn't seem to be the case in anyone else's experience). And when else could they have expected Ben to have been stung? Unless Grievers are walking through the Glade (and at that point, they weren't) the only time Ben would have been out would have been during the day -- he couldn't have gotten stung at night.
In the books, the Gladers have the Swipe a microchip that allowed WCKD to wipe their memory AND control them directly. The second movie shows that the Gladers are chipped for identification, and implies that the chip is related to the memory loss, but nothing has implied that they control the Gladers. The Grievers are also shown in the movie to be controlled by WCKD electronically.
Either way, it would have been simple for WCKD to arrange for Ben to be stung, simply by having a single Griever attack quietly in the Glade. Keep in mind that WCKD has essentially unlimited funds and created the Maze from scratch. They could have easily built a tunnel for the purposes of forcing this event from the beginning. The entire Maze trial was planned out in detail.