FULL PRODUCT VERSION :
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

(
Not entirely sure, as the application has an embedded version )

ADDITIONAL OS VERSION INFORMATION :
MacOS 10.12.4

A DESCRIPTION OF THE PROBLEM :
When using a apple magic mouse clicks do not always register within a java application. Switching to a wired usb mouse fixes the problem. Apple has stated that this is a problem with Java and not in macOS


REPRODUCIBILITY :
This bug can be reproduced always.

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This is with an application not written by me, I am a user trying to figure out if this is a problem within Java or if the developer just writes poor code. Please let me know which is the case as I have not been able to find many people complaining about this.
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CUSTOMER SUBMITTED WORKAROUND :
Use a wired usb mouse and not an apple magic mouse