The Home Office Deduction is being disallowed because the program says there was no profit, yet we have 11,000.00 of taxable profits. How can we fix this error?

Did you assign it to the same schedule C?  

And you have to answer yes to both questions about exclusive and regular use, not just one.  The area of your home office must be used regularly and exclusively for business to deduct it.

Or you checked the box on 32b saying Some Investment is not at risk.