If you use KoLmafia's built-in Tower script, it uses the expected combat item to kill the monsters.
If you are killing the tower monsters without items, you are ascending the tower manually.
Are you saying that KoLmafia made an NG for you when you manually clicked on the tower? I wasn't aware it did that, but, that seems reasonable; if you immediately encounter a globe and don't intent to kill it abnormally, you will waste a turn by running away if you don't have an NG.
But if it makes an NG and you manually climb the tower and find the globe and kill it without using the NG, well, all you have to do is untinker the NG to retrieve your letters. I am sorry it "cost you a pull" because you forgot about the Untinker - but that is hardly KoLmafia's fault, is it? At most, it "cost" you 10 Meat for a meat paste.