When it list my taxes withheld it is incorrect. I put in my military pension with the taxes withheld but it doesn’t include these taxes in the final recap

Go back and revisit the 1099R.   Tax withholding should be in box 4 and will show up on 1040 line 25b.  If it’s not working then delete that 1099R and enter it again manually.  That usually fixes it.  

You didn't actually pay the tax.  You had taxes withheld like from your paycheck. You still have to enter the 1099R and whole gross original amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding is subtracted from the total tax to figure your refund or tax due.  The gross amount shows up,on 1040 line 4a or 5a and the taxable amount on 4b/5b. The withholding will show up on 1040 line 25b.