The Gap sent a similar response to people via e-mail:
Gap Inc. spokesperson
But people investigated and found the shirts still on sale in some stores.
Gap's Colonization clothing line
Also, the Gap was selling related t-shirts online. These seem to be part of an "American Frontier" collection, with slogans such as "Onward," "Roam Free," and "Exploring East-West." These might not be a problem by themselves, but next to the "Manifest Destiny" shirts, their messages are suspect.
For more on the subject, see McNairy "Hurt" by T-Shirt Criticism.