There are two ways of using "唯一问题就是"

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.