I am unsure if this is intentional or not, but when you toggle the additional skill in skill upgrades area the icon to turn it back on disappears. Took me a bit to figure out how to turn it back on.
I have attached what I am talking about below to further clarify. Thank you :)
On/Off Button Disappearing
https://i.gyazo.com/27b0b976fe771337e5670da1e5e6ea6f.gif