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 .