Or the fireproofing on the beams was in the middle of being removed and replaced, and/or was severely deficient in a number of spots.

Fireproofing is a cementitious spray that gets applied to structural steel for fire protection. It's largely an inflammable coating, but also serves to keep steel cooler in conjunction with sprinkler systems. In a normal fire, the sprinklers will wet the fireproofing, making it harder for the flames to heat the steel, which causes elongation and ultimately failure.

Bond coefficients were found to be weaker than the minimum requirements. Granted, a plane smashing into structural steel will most likely knock fireproofing off of steel, rendering the system useless, but if the fireproofing applied can't stick to the steel it's worthless.

Fireproofing was also found to be deficient at beam to core connections. The core of the building was where all stairs and elevators were. Beams supporting the floors were connected to the core with steel angles. The fireproofing was found to be insufficient in these areas, meaning that it probably wasn't thick enough, as per building codes and manufacturer's specs. It probably failed well before it was intended to. Then again, nobody had planned on planes flying in and fucking up several floors at once.

True story, I'm in construction and deal with fireproofing on a pretty regular basis. Whenever a contractor tells me not to worry about the fireproofing, I bring up the twin towers.

Other true story. I watched them fall from my history classroom window in high school. That sucked.