We had one substitution when DD9 took the WPPSI-III years ago. It was because her score on the Picture Concepts was way, way lower than her other scores. The tester said, "In spite of standard practice examples and extra explanation, apparently this task was unusual enough that DD did not grasp what she was expected to do. Because of the discrepancy between her score on Picture Concepts and the other visual reasoning subtests, an additional supplemental visual subtest, Picture Completion, was administered to give a more complete picture of DD's visual reasoning abilities. Her score on Picture Completion was highly commensurate with her Block Design and Matrix Reasoning Scores, supporting the view that her visual reasoning ability is very high, but that for some reason she did not comprehend the task on Picture Concepts." (She got an 18 or Block Design, a 16 on Matrix Reasoning, a 17 on Picture Completion ... and a 3 on Picture Concepts.)

I don't know if there are other reasons that they substitute besides a spoiled subtest, or how they decide. I've only heard of it being done after the fact, the way it was for DD.

One link I found online says that you can only substitute in the case of a spoiled subtest or if there is a temporary reason that a test cannot be given (e.g., a broken finger). That's for the WPPSI, though - I don't know about the WISC. This link says
Quote
Additionally, there may be some characteristics of the child being tested that would warrant subtest substitution. For instance, a psychologist may be assessing a child with significant fine motor difficulties. In this case, the child’s WISC-IV Processing Speed Index score may be unfairly impacted because the WISC-IV Coding subtest requires a degree of fine motor coordination. As a result, it would be acceptable for the psychologist to substitute the WISC-IV Cancellation subtest score for the WISC-IV Coding score. The WISC-IV Cancellation score does not rely as heavily on fine motor skills and may therefore provide a better measure of processing speed for this particular child.

But it still strongly advises against substitutions in general.