פירוש על קידושין 63:9

Those to be burned [became mixed in] among those to be stoned: It is implied that one [person] who was to be burned was mixed in with many to be stoned. And we have established it (Sanhedrin 79b) [that] all those liable for death penalties in the Torah that became mixed up - and it is not known which of them are with the lighter [punishment] and which with the stringent - are all sentenced to the lighter. For you are not permitted to move over the light to a stringent punishment for which one has not become liable.

Rabbi Shimon says, "They are judged with stoning": As it is lighter, for Rabbi Shimon [holds that] burning is more stringent than stoning. And the reason is explained in Sanhedrin (50a).

According to R. Shimon, burning is a more severe penalty than stoning. And since the court cannot give a condemned criminal a worse death penalty, they must all be executed by stoning.