On the 941 Form, line 2 is wages subject to FIT (Federal Income Tax), line 5a is wages subject to FICA and line 5c are wages subject to Medicare.
If line 2 is less than the others, you have employees marked as exempt from FIT or they have deductions being withheld that are exempt from FIT.
The 941 instructions tell you to enter the taxable FIT wages that will be displayed in box 1 of the W2 Form.
And the W2 Form show that it is the taxable wages, not the gross wages.