1. common usage:
When almost all the puzzles are solved, there is only one easy piece left.
Example: All the dishes are ready, 唯一问题就是waiting for little rice to come back with sauce.
2. jokingly
When a major part of the the puzzle is still needed to be solved and there is no solution yet. Laughters are usually expected.
Example: Ate over le, 唯一问题就是waiting for little rice to pay the bill.
Apparently, the first usage was the author's intention; however, logically, it does sound like it fits the second usage better. Not knowing whether it is used jokingly causes readers not being able to decide whether to laugh.
