The total self employment tax on my transcript is lower then what I paid when I filed, which is listed as the "tax per return". I'm wondering why the numbers are different.
They are different because they correspond to different line items on your Form 1040.
That is not a reason to amend.
Additional comment:
The tax per return? that is likely the SE Tax PLUS the regular income tax added together.
i.e.
1) Your tax return calculates an SE tax based on your self-employment income. That's one tax value, but is just the Medicare and SS tax for your SE income.
2) Then the tax return calculates the regular income tax based on your total income from all sources.
3) Then the total tax you paid is supposed to be #1 + #2 added together. (plus any penalties if you underpaid during the year).
Thus the tax you paid (#3) will commonly be greater than your SE tax . In some instances it may be the same as your SE tax value, but only if your income is so low that your Std or Itemized deductions wipe out the regular income tax portion from #2.