ROB, Sonic, Fox and Sheik are the ones I'm having trouble with right now, and I think Diddy isn't even that hard lol (is still a bad matchup for Bjr tho).
ROB can keep you at a distance with his projectiles, tilts and grabs. Recovering high can be met with a good laser or gyro throw and recovering low can be a potential gimp or spike.
Sonic is just too fast for Junior to do anything offensive effectively and grabs seem nearly immpossible in this matchup.
For Fox and Sheik, they are also too fast for Junior as well and they can combo the hell out of him, grabbing is hard as well.
This is based on my experience playing offline against good players in my region.
I think ROB is more my problem rather than the character (at first I thought Villager was hard as hell but I learned the matchup by now), learning patterns doesn't seem to work if the ROB is good and always mixup things.