I think there were signs that Neal was still in love. While walking on the beach with Emma last season (i think it was episode 21 or 22) Neal mentions that he regrets leaving Emma in jail. He wished he went back for her but he never did. The only reason he didn’t go back was because he was scared that Emma wouldn’t want to see him anymore.
Emma, rightfully so, in fact did not want anything to do with this man! So, if anything I think it’s weird for HER to still have feelings for him when she has experienced what Neal put her through.