There can be several reasons you may have issues seeing items in your inventory.
Due to the large amount of inventory slots you can have, it may be difficult to see one specific item due to similar looking items. To assist in finding an item, you can Press CTRL+F and then a field on the bag UI will open up that you can fill in with the name of the item. This will black out all items without that name and allow you to very easily see the item in your inventory.
Another issue that can occur is that your bags may be moved on top of one another. To see if this may be the case, open up all your bags and move them around to see if they are on top of any other bags. If you find a bag underneath another bag, you can reposition them to locations on the screen so they are not on top of each other.
Something else you may see is that quest items will be added directly to your quest inventory. You can access this by pressing L to open your quest log and look along the bottom of the quest UI.
There are also some items that are consumed automatically, such as Crystallized Insights or Writs for titles, and will never actually be in your inventory for you to look at or use. When they are automatically consumed they will be added directly to your character instead of your inventory.