like the previous answers are saying, you are tempering with list2, in other word when you do for number in list2, you are taking 7, 8,9 but never using them, but instead you are removing 12, 11, 10 from the list and printing it. you could do it this way instead:
    for number in list2:
    #Unless you want to append in reverse order(see below for that)
    #comment the next line
        #nextnumber = list2.pop() 
        print ("Adding number ", number) 
        newlist.append(number)#Append the number you just got from list2
    print (newlist)
  out[:]: ['one', 'two', 'three', 'four', 'five', 'six']
  Adding number  seven
  Adding number  eight
  Adding number  nine
  Adding number  ten
  Adding number  eleven
  Adding number  twelve
  ['one', 'two', 'three', 'four', 'five', 'six', 'seven', 'eight', 'nine', 
  'ten', 'eleven', 'twelve']
If you want to append in reverse order, do what @thachnb suggested.