I checked everybun over today. Penny has 2-3 toes with this bump on it on her front paws. When I touch it, she doesn't seem to react in pain or otherwise. Kirby has red bumps on about 2 toes on each front paw as well. Kirby reacted rather strongly when I felt them, but he was very jumpy to begin with so I'm not sure if it was a pain reaction. Toby has 2 toes total with this bump. I put some neosporin on the bumps as best as I could. The bumps were buried in fur but didn't have any fur on the bumps themselves. Nobunny had bumps on the hocks/rear feet.
Here's a better picture of the bump on the bottom of an affected toe.