Speculah:Witches are generated by Magical Girls
There is possibility that the witches are generated by the birth of magical girls. That means the wishes can generate anti-wishes related to magical girls themselves. For example, Mami's enemies are related to flowers, butterfly, desserts. Mami has interests on desserts and she also uses butterfly-like hair clip. The theme color of the witches' lairs is close to Mami's theme color. When Sayaka becomes a magical girl, the witches' lairs change to blue theme color. The stronger wishes generates stronger anti-wishes. As a result, possibly Madoka could generate very powerful witches.
The opposite could also be possible: a human turned into a witch by making a curse generates an "irregular" magical girl with an anti-curse. This would then be why Kyubey can't track Homura; she never accepted the contract.