This is by design. According to the IRS instructions for line 11 of Form 4562:
"Enter the smaller of line 5 or the aggregate taxable income from any trade or business you actively conducted ... Include in aggregate taxable income the wages, salaries, tips, and other compensation you earned as an employee (not reduced by unreimbursed employee business expenses). If you are married filing a joint return, combine the aggregate taxable incomes for you and your spouse."
Based on this, you should include income from all businesses and employers for the taxpayer and spouse in each taxpayer's income for the limitation.
This information applies to all years of the UltimateTax software.