Those items were designed to take players from level 90 to level 100. After the level squish, they were 1-39, then the next upgrade go to 44, then 49 or 50. Interestingly, the Wowhead link shows no change from level 2 to 3. 
Anyway, these items are designed to be upgraded three times. Look at it this way: since they start at 39, they essentially start with two upgrades.