"I wish Jon had a different mother." Zelda wished, sure the rock would solve all of her problems with Jon's family.
The issue she didn't foresee was the same mistake Jon had made. The word "had" being past tense could be taken to mean that he already "had" a different mom in the past. In most cases Linda Madison would automatically be replaced.
In this circumstance Jon considered himself to already have a different mother, now that Sarah McMillian had assumed the role.
It could also come to mean a different mother than he had ever had before.
With Zelda unaware of the family swapping wish there was no way for her to know the slim chance of Sarah staying as Jon's current mother.