At 16 weeks old, a sore tooth is not out of the question as Maura pointed out........teething and losing teeth is probably the issue if he just started this not wanting to chew his kibble.
Maybe you could take a peek in his mouth to see. Also, some frozen stuffed kongs might feel good if teething IS the source of the problem
Not all dogs can be free fed, even if they are the only ones in the house, LOL, Phoebe would do fine, Orson would explode himself before he stopped eating.