This one is relatively minor but because it happened to such a prominent landmark, I'll throw it in.
For a period after it's construction, the John Hancock Tower in Boston was known as the Plywood Palace because of a design flaw in the windows which meant they had to be replaced with sheets of plywood temporarily.
http://www.universalhub.com/node/24883
On top of the window problems, it was also found that the tower could be blown over on the narrow side, so extra bracing had to be added.
http://www.glasssteelandstone.com/Bu...Detail/399.php
Also in Boston, a building along the waterfront rather dramatically settled suddenly 12 years after it was built because the concrete in the foundation had simply dissolved away.