Nothing is wrong. You MUST refill completely. I believe it states this in the manual.
I tried doing what you did - only adding 2.5 gallons to the 5 gallon tank when the end-of-the-world messages started. But the messages did not go away, even though I waited several days. So I bought another 2.5 gallons and refilled it and THEN the messages stopped.
Then I called my Ford diesel truck service manager and he confirmed that you must refill it completely to stop all the messaging.
But here's what I am not clear on. If the message comes on, and you only partially refill, will it indeed go into limp mode, etc, even though you still have 2 or 3 gallons of DEF in the tank (for example). I never got a good answer on that. But I'm sure not taking any chances.
So I think Ford needs to redo how the sensor and alerts work together. If you add DEF above a certain minimum level, it should not continue the countdown until it gets back down to the danger level.
So now I carry 5 gallons of DEF with me at all times (full timing). And I'll also fill up with DEF when fueling up if I can.
Tim.