I'm not saying he didn't get infected by the facehugger.
Granted, this is more from the Final Trailer than the ending of S1.
1. From my perspective, there is an intended link being drawn between the relation of Will and the hydra. This plays parallel to El's relation to the Demogorgon.
2. El mentioned in S1 that she was unable to visit the UD as she wishes. Will seems to have no trouble doing so.
3. Will has a "blank out" in the field where the crew + Joyce are all asking him and he just seems spaced out, very smilar to El's reaction after the contact through the ham radio in the AV club office. He looked blank and drained.
4. Will is obviously being subject to tests and experiments at the Hawkins Lab. With Hawkin's history, I would bet that these are at best clandestine ways to get more data off a subject since El isn't around and they just happen to be masked behind helping the Byers' after Hawkins' cover up.
5. Hopper is rushing Will out of a lab (probably Hawkins) in a hospital gown thats similar to El's from S1.
6. Will is not in the "arming up" shot at the end of the trailer and everyone else is.
7. Mike claims that if "anything can destroy this, it's Will." Drawing another link between how El/Demogorgon and Will/Hydra seem to share a connection.
Trying to find the best way to simplify this. If El's ability is the result of the experimenting on Terry Ives, Will could easily have gained some similar talents after being exposed to the UD for so long. El's had her whole life to learn them, where Will's seem to be chaotic, intermittent, coarse, and unpredictable. Chaotic good vs Chaotic Evil to bring home the D&D references.