Some ideas on Hogan working at the Pentagon while it was under construction:
Hogan talks about doing paperwork at the Pentagon. The plans for the Pentagon started in early 1941, and the ground breaking was on September 11th. But the design was still be revised at the time. As a Col in peace-time, he might have been assignment to serve as a USAAF representative - their voice in the design of the Pentagon. Each branch would have had multiple represenatives to ensure that their requirements and concerns were being addressed. This would have resulted in a lot of paperwork (which he would then send to Col. John Smith).
Also, at the point when he is telling this story, the Pentagon was fully operational with most of the units moved out of the temporary munition buildings on the Mall. So it might have just been easier and less confusing to say that he was working in the "Pentagon" instead of "Munitions Building that served as the Department of War on the National Mall."
Finally, it could just be outright misinformation that Hogan is feeding Klink, since it seems that Hogan would be too good of an officer to resort to misrouting paperwork. And if challenged by Klink, "But the Pentagon didn't exist then!", Hogan could reply "and neither did Col. John Smith!"