Victor skills upgrade bug

In my recent game with victor i had (The Hex Core mk-1) then bought (The Hex Core mk-2) it showed that i can upgrade 1 other skill, but i didn't.... i waited for gold to buy (The Perfect Hex Core). when i bought it, it shows that i can upgrade 2 of my skills ... i tried but only 1 skill was upgraded. thus i completed the game with incomplete upgrades and with no clue how to fix that.

Please inform me if i made a mistake :)

Regards.