Tax software only 'acknowledges' what you, the preparer, enters.  So, you told the software your clients are non-residents.

Tax software doesn't 'charge' anyone income taxes; the software computes the tax based on what you, the preparer, enters as income sourced to Delaware.  

Review your data entries as to what is/is not Delaware income and whether you've coded it as such.

In Lacerte (PTO's big sister), there's a drop down menu by the income items to tag what state the income is sourced to .

A nonresident of DE will pay DE tax on their DE source income. I presume there is some, or else you would not have added DE as a state.

Are your clients a corporation?  "All corporations incorporated in the State of Delaware are required to file an Annual Report and to pay a franchise tax....  For an Annual Report or Amended Annual Report for non-exempt domestic corporations the filing fee is $50. Taxes and Annual Reports are to be received no later than March 1st of each year. The minimum tax is $175.00 with a maximum tax of $200,000.00."

https://corp.delaware.gov/howtoform/ 

My guess is that someone went to a seminar where someone told them that a Delaware corporation is a status symbol that will help them get dates.  But I could be wrong. 

Of course there is always the possibility that you thought wrong.