Retirement tax questions

I assume that you are speaking about seeing this screen:

You see this screen because you have a code 2 in box 7, so there is no penalty on the early distribution from the pension.

However, you still owe tax on the distribution (i.e., the distribution is added to line 5b on the 1040), UNLESS you rolled it over to another retirement account - in which case the distribution would not be taxable (i.e., not on line 5b). That's why there is the difference in the refund.