The answer may vary slightly depending on how you implement your custom call bubble. This / was the solution I am using: Customize the MKAnnotationView callout , and I ran into the same problem.
Basically, every time a leader is displayed, I had to move the subview to the foreground.
In this case, my custom call bubble is a class called "BaseCalloutView" that contains the UIView as its ContentView property (as you can see in the UML diagram from the link above). When the annotation is selected, it runs the animateIn function from BaseCalloutView, to which I added:
[self.superview bringSubviewToFront:self]
As I mentioned, your mileage may vary depending on how you implement the custom call bubble. I can provide you with the full code if necessary, but to be honest, 90% of my code is located at the link above.
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