So at Level 9 the Armoror gets the ability to infuse each piece of their armor separately and in addition also receives two more uses of infusions along with it, as shown below on the ability description. 

9th-level Armorer feature

You learn how to use your artificer infusions to specially modify your Arcane Armor. That armor now counts as separate items for the purposes of your Infuse Items feature: armor (the chest piece), boots, helmet, and the armor’s special weapon. Each of those items can bear one of your infusions, and the infusions transfer over if you change your armor’s model with the Armor Model feature. In addition, the maximum number of items you can infuse at once increases by 2, but those extra items must be part of your Arcane Armor.

However, on the character sheet after reaching level 9 it does not add an additional two checkboxes to track uses. Since these extra uses are supposed to be solely for the armor I thought they might be listed under the Class Features but while Armor Modifications is listed there's nothing there to track as well. Is this a bug or has it just been overlooked? 

Since they more fully integrated Artificer infusions in the Inventory section of the character sheet, the system now actually automatically tracks and caps a character’s infusion limit there. When you hit your limit the system won’t allow you to infuse any more items unless you manually click the [OVERRIDE INFUSION LIMIT] button. Since that functionality has been so significantly upgraded compared to how it used to work, there really is no need for those checkboxes under Features & Traits at all anymore. (At this point they are as vestigial as an appendix, and just as unnecessary. I actually forgot they were there I haven’t used them in so long.)

Since those particular upgrades happened before the final Armorer subclass was published, the DDB Devs probably forgot about them too. In fact, it wouldn’t surprise me to learn that it wasn’t so much a matter of them forgetting to add those two extra chackboxes for the Armorer subclass, but rather them forgetting to remove the original checkboxes from the base class feature.

Edit: I will however point out that the Armorer’s Armor Modifications feature is completely lacking a snippet and therefore displays absolutely no information whatsoever on a character sheet.
     (Whoever did the snippets for the subclasses in Tasha’s Cauldron didn’t meet the typical standard I expect from DDB. I recall having a couple of “WTF moments” regarding some of the Feature or Action snippets for some of the other subclasses from that book as well. Maybe it was the Aberrant Mind or Fathomless or perhaps the Soulknife, I don’t really remember anymore.)