I'm sorry. Concepts like this are so simple to me, I forget it should be explained better.
The heat in the lower levels of the building rose such that the steel lost it's full strength. Think of butter. It is a solid when refrigerated and soft at room temperature then melts when it gets hotter. Steel is like this. It gets soft without melting. It slowly changes shape. Horizontal beams will sag, pulling vertical beams away from perpendicular. Buildings do not fall from this alone. However, if you have a single missing supporting beam, the structure can shift enough to completely lose integrity and fall apart.
As for the windows. The sagging of the steel beams would only have to be maybe an inch or two interrupting the 'squareness' of the building. With the widow frames no longer being square, the windows shatter from the stress because they are a relatively brittle solid.