Lost Passive Skill Points on Respect

I refunded 3 skill points (Coming Calamity, Herald Damage, Herald Damage) and applied them in a different area for some more generic stats and a jewel slot, but upon confirming the refund I was only refunded 1 skill point but had lost all three of the perks I refunded. I am now down 2 skill points and very sad about it.

Is there anything I can do to resolve this?