Dont forget you need the following to purchase the clan skill upgrades:
1) a high enough unit level to unlock the upgrade (e.g. level 5)
2) enough unit skills to unlock the upgrade (e.g. 4 seperate skills)
3) an unspent unit skill point (from recent experience gain)
4) enough clan skill points (e.g. 20) (see avatar page)

I kept trying to upgrade without #3 and/or #4 and thought it was broken-- but you need to have the clan skill points as well as an unspent experience point, as well, plus all the unlocks. Hope this helps.