Make sure you finish the Kindergartener's Hide and Seek quest. You should also try to find the Woodland Critters in the Lost Forest. Someone made a guide on Steam that shows where all the friends are. Here is the link (MAJOR spoilers):
I wonder if I had an issue with the checkpoint saving, because I had all of the friends on the list except the Chinpokomon company.
I've read of others having similar issues, except with disappearing items. I believe the cause of this was insufficient disk space.
Another theory is that you didn't reach a new checkpoint before exiting the game. Thus when you reopened the game, it loaded the most recent checkpoint, which might account for the missing friends. I always try to use the quick-travel system before leaving the game. This usually triggers a quicksave. Lookout for the Wellington Bear tape recorder icon on the bottom right hand corner of the screen. This is the save icon.
Edited by Shirobon, 14 March 2014 - 07:18 PM.