While Tim's answer above is technically correct, it seems like quite a bit of code to me.
I would assume that to remove a patient from the list, you already know that list and have a reference to it at the time you want to remove the patient. Therefore, the code can be as simple as:
id myPatient = ...;
id myList = ...;
[[myPatient mutableSetValueForKey:@"lists"] removeObject:myList];
This is of course assuming that your relationships are bi-directional. If they are not then I strongly suggest you make them bi-directional.
Lastly, because this is a many to many relationship, you can execute the above code in either direction.
[[myList mutableSetValueForKey:@"patients"] removeObject:myPatient];
update
Then the code is even simplier:
[myPatient setLists:nil];
That will remove the patient from all lists.