Karma Houdini: Sarah Genatiempo. Not only was she the mole for The Order for the WHOLE DAMN TIME, she also pulls off a Face Heel turn in the finale of the series to date, with no sign of comeuppance in sight, betraying both Jonas and Maggie to their fates
Though there are quite a few fans who file the whole Resistance series under FanonDiscontinuity, given the sheer Ass Pull nature of the reveal.
The ending. Some people liked it, while a majority of the fanbase thinks it's the worst ending in the LG15 franchise. It doesn't help EQAL announced a season 2, but was never materialized due to the economy and not making another LG15 show or even mentioning Lonelygirl15 since LG15: Outbreak in 2010.
Fanon Discontinuity: What was supposed to be the season 1 ending but became the series finale due to EQAL not making another season, to a lot of fans.