How do you indicate to TurboTax that a distribution from a qualified pension plan was not hurricane related. there is no was to check the box.

Go back through the entry of your Form 1099-R. 

You will get to a page "Relief for hurricane or wildfires distributions" where you are asked, "Was this distribution due to Hurricane Harvey, Irma, or Maria or the California Wildfires?"  (See the screenshot below)

Answer No.