I have noticed that there is an issue with the Skills tree counter. For example it tells you the next level = 10, then you click it and it takes 11? Sometimes all you have is 10 and the + is active and you click it and will not let you use the 10 points even though it says 10 and is active. It wants 11 points? It does this all the time on every level for every skill…? If it wants 11 it should reflect 11 and not say 10 and give you the option to click at 10 (for example). This has caused some issues when balancing who gets what. If you can see the correct number it would not be an issue but this makes it to easy to mess up, please fix this!
Attribute increase buttons? Strange, haven’t noticed that. For me they work as usual.
No watch it carefully when you assign skills it will say (for example) 10 needed but when you click it it takes 11 always adds one extra to the take. BUT… in the odd occasion it does not? I can’t figure it out, but at least 4 out of 5 times it will always take one more then advertised!
I watched it carefully just before posting to be sure if I’m not mistaken. 
You must have encountered some bug which is not present in my version.
Don’t get confused with the skills button and the abilities button… The skills I am talking about are for will power, strength etc… this is were it is wrong! The abilities (icons) work fine they are always the right count as far as I can see…
Are you sure you are not confusing the stat amount to the SP cost amount. Say like in this picture, the STRENGH stat of 14 will cost the highlighted 7 SP points to give point to… and you would get 7 SP back if you could lower it to 13(as shown in the other side of the picture, which cannot be done without usage of mods, as this is the hardest difficulty start):
The speed and will point cost stats are close to be the same, while strengh is not, so I picked as the example.
This is with the graphical User interface enhancement from the Terror from the Void mod, which adds the green and violet colored amounts from equipment etc add-ons.