I had a guy who used a Sentinal and then used the Armour Piercing Feat Card. Is this legal?

This guy just kept using the multi attack and kept giving 1 pt of damage.

Just wondering since all these giant figures have certain innate powers that can't be used on them....this seems to be a little unfair?

Yep. As long as you it meets any pre-req there is currently no rule against using feats on Big Figs.