Duplex Outlet-Open ground only on top
It is not controlled by a switch and I didn’t break any tabs.
  What could make this happen?



Debris inside the socket of the ground conductor
A defectively manufactured outlet



  Is it safe to use the outlet or just the bottom of the duplex?


Safety is a relative thing.


If you use the ungrounded top outlet it will be as safe as older houses that were built before grounding was a thing, and were considered safe in their time.  It will also make no difference for two prong appliances.
If you crazyglue an outlet protector over the top outlet to prevent use of the top outlet, then it will be as safe as not using it.
But maybe the DC converter will short to hot and electrify the phone someone is holding up to their head.


I say take it back to the store and report the fault and get an exchange.  

You got a product that is less than it should be.  Safety or not, you'd return a plasma tv if it had lines down it or only received even channels.  Return this outlet too.


  Do outlets with USB ports show open grounds?


Only busted ones.


  would putting a GFI outlet in that box assure it is grounded?


Nope.  GFCIs do not create ground.

Changing the part out (with a gfci, or with any other outlet) would most likely solve the problem though.  And in a kid's room, I think a GFCI is worth more than USB outlets if its a kid you want to keep. 

Perhaps consider installing one GFCI in the "first" outlet box in that room, or in what ever the next closest junction before the circuit enters that room.  Then USB outlets inside the room.  In 60 seconds of Googling, I could not find an outlet that had GFCI and USB in one.  You could also use a GFCI breaker but those are a pain in the neck.


  something I may be missing


The receipt for that usb outlet, and its original packaging?  With that, you should be all set.  Let the clerk know it is dangerously faulty so they think longer before re-shelving it.  If you get another of the same model and it has another fault, then you should tell us what model it is so it can be avoided.  Good on you for testing the outlets after installing.  I haven't done that on nema 5's in a while....