It seems its an undocumented feature of update 14.
Try resetting you skills tree as was suggested.
Hey! I'm having the same problem too! i have enough marks, so i bought it twice because i thought you were supposed to (i realized that that just means it updates the level of training and you're not required to keep buying) but even so, when i go to TOM after i buy it from WILL, i can't slot it and press 'Confirm' because i have this 'unfulfilled' pre-requisite and i don't know how to fix it.
i'm pretty bummed--this is the first time i'm every trying out skirmishes and i can't progress of course until i complete the tutorial. i hope this is something i can fix/something that will be fixed soon...
if anyone has any solutions i would LOVE to hear!!