They do not pay your working hours, probably because you didn't keep them updated about your working status of the project.
As a contractor, you do not have to fix every problem fast, but you need keep the manager informed.
This way, even the problem was not solved by you, they still pay you without questioning.
In your case, apparently, you didn't convince the boss you spend time which is worth them to pay...
Please make improvement in next job. Thanks!