Jonas was upset during the Ceremony of Twelve because of the sudden break in the traditional order of the ceremony. Jonas is already anxious in the time leading up to the ceremony, as he is eager to know what his Assignment will be, even though he doesn't have as much certainty in the specifics of it as his friend Fiona (who is a naturally caring person and will certainly be given a position as a Care Taker).
Fiona is assigned to be Number Eighteen, while Jonas is assigned to be Number Nineteen. The ceremony works by proceeding chronologically through the numbered children. When a child's number is called, he/she will be praised for his/her strengths and given his/her Assignment.
After Fiona is given her assignment of Care Taker of the Old, Jonas expects to be called next; instead, The Chief Elder skips his number and moves directly on to Number Twenty. Jonas realizes that The Chief Elder does not make mistakes and that he must have been skipped on purpose, which strikes immense fear in his heart. He figures he must have done something terribly wrong. In reality, he has simply been chosen (not assigned) for a more important position: that of The Receiver.