Checking the box for qualified business income causes my taxes on Turbotax to go up! How can that be?

Both my wife and I have Schedule C businesses (not incorporated) in addition to wages from jobs.  If I check the box "yes" for my wife's Schedule C for "qualified business income", our taxes calculated by TurboTax goes down -- as I would expect since it is a deduction.  But then, oddly, if I check the same box for my Schedule C, our taxes jump up hundreds of dollars.  What is wrong here?  How could qualifying for a deduction by checking yes raise our taxes rather than the other way around.  Is this a bug in Turbotax?