It's a little jarring to find two identical enchantments on an item.

Are you using any other mods?

Apotheosis and Champions to drop random enchanted items. What I'm seeing is that canApplyTogether(Enchantment ench) has been overwritten to just return true, when in vanilla it returns this!=ench. Is the overriding intentional?

Fixed in 6e1a1eb, but Apotheosis also will ignore this from time to time, just so you know!