Once you have opened the Global Library UI, right-clicking a bread, egg, pickaxe, and possibly other tools and items will make the inventory restore the state prior to the opening the Global Library UI, sometimes overwriting items. Reloading the world fixes it.

The bug is exact the same from Exotic Birds (now fixed): http://www.minecraftforum.net/forums/mapping-and-modding/minecraft-mods/1282698-exotic-birds-peacocks-woodpeckers-phoenixes-owls?comment=908

Video: https://youtu.be/MmbFPDF1wds?t=21s (simply replace the Exotic Birds UI with Global Library UI, the issue is the same)