It helps if you can post your project here so people can see what could be the problem.
I understand what you are saying, but it isn't possible for me to do that. We are working on something confidential in nature. The project is also very complex and wouldn't make much sense without a lot more information.
I assume you are using the ISR signal.
I guest you enable the interrupt some where during initilization.
One thing you can check is NOT enabling the interrupt at all, comment out all enable of the interrupt and see if that is still firing.
do you have enabling the interrupt in mutiple places, if that is the case, you can add a counter to count if your have matching enable/disable pairs.
In an ISR-configuration you specify how an interrupt is triggered. That implies (for some modules) that you have to reset the int-reason. This is normally done by reading a status-register of the component that signaled the int.
Which device are you using and which silicon-version Is there an ES? and which?
Also be aware of the fat that in PSoC, the actual ISR source can be a hardware signal and by connecting an ISR component you are assigning an interrupt vector and a priority to it. In addition to disabling this interrupt it might as well be required to kill the source of this interrupts to isolate the problem. Try to disable the source(some hardware signal in your design) of this interrupt and see if it gets resolved.