Whenever you use a currency on Kraken, it will leave an entry for that currency in the Balances table on the Trade > Overview page.
Even if you spend or withdraw 100% of the balance, the currency will still be listed on the Balances table. This is so that you can easily see which currencies you've used with our platform.
It should not be taken as an indication that you have dust amounts in these currencies.
You can hide the zero balance currencies from the balance overview with the "Hide zero balances"-button.