iOS 9.3 - Some of the map annotation disappears with customView

Description:
I have a map with custom view. When I try to zoom in/out the map, some of the map annotation disappears. This happens on iOS 9.3. It works as expected on iOS 9.2.

Environment:
Appcelerator Command-Line Interface, version 5.2.2
Mac OS X Version = 10.11
Node.js
Node.js Version = 0.12.7
npm Version = 2.11.3

Appcelerator CLI
Installer = 4.2.4
Core Package = 5.2.2

Titanium CLI
CLI Version = 5.0.6
node-appc Version = 0.2.31

Titanium SDKs Version = 5.2.2
iOS version: 9.3
Physical device: iPad

Test Case:
Test case attached with this ticket

Reproduction:
1. Create an alloy project with the attached test case
2. Run on device
3. Zoom in and out the map several times

Actual: Some of the map annotation disappears
Expected: Map annotations should always be visible