Haste, Two-Weapon Fighting, and Natural Attacks

[Jobe00]

Friday night, my Arcanist/Rogue (Unchained)/Arcane Trickster with +5 BAB and TWF cast Haste. According to Hero Lab for iPad, both my Main Hand and Off-Hand shortsword attacks got an extra attack at highest (and only) Attack Bonus.

Meanwhile, a Badger Companion with Bite and 2 Claw attacks and a Wolf Companion with only a Bite got no additional attacks.

By the rules as written, the Arcane Trickster should have only gotten an extra attack at highest bonus with the Main Hand and the Badger and Wolf should have gotten an extra Bite.

I'm going to guess Multiweapon Fighting might have the same flaw, but I haven't tested it.