Plot hole: The watch that is presented to Collier by Elise which starts this entire story is never purchased, stolen or acquired in any way, but left behind by Collier. It is just there, which is a paradox in itself.
Plot hole: When the fog finally hits the lighthouse and is seeping in, the generator is hardly audible vs. how loud it was when it was first started.
Plot hole: Lois and a friend of hers are watching Non and Superman fight. But this is totally senseless, because Superman had been flying around Metropolis and chances are slim that he appears in the very same spot to let Lois watch him. And, second and most important, should any doubts arise, the panning angles of the camera never show Lois's building, with the big broken window and the flag poles.