If you notice that you have some items are are not being taxed at the point of sale, it is most likely means your tax rule has been set up with a filter, and the item does not match the filter.
For example if you have a custom field called "department" with values "Clothing, Footwear, Accessories" and you live in an area where only clothing is taxable, you would filter your tax rule to say that only items with the department set as "clothing" should be taxed.
Now, if you forget to mark an item with the department "clothing" this item would not be taxed at the point of sale. Once you edit the item record to set the department to clothing, the item should be taxed.
For more information on how to create a tax rule, click here.