So I don't know if anyone else is experiencing this bug, but I figured out a way to fix it and I'd figure I let people know.
In New Leaf, it's possible that nothing will show on your encyclopedia, though characters will react to it as being updated and your PC won't prompt you to check it with every catch, just new ones. This is most notable when you're trying to get through the early game tutorial with Isabelle, and she asks you to find three fish (or insects I'm presuming).
Fortunately this is an easy fix! Just press any of the empty squares, then switch to another tab and then back (from fish to insects then back to fish, or any other switch). Your information should show up, safe and sound! This seems to be an odd one-time glitch, so I figured I'd let people know.