It sounds like you have set up your Interrupt Service Routine and you are making a direct function call to the same routine; eg,

void isr(void) interrupt n
{
   // Handle the Interrupt
}

void main(void)
{
  isr(); // Direct call to Interrupt Service Routine 
}

You must not do this!

The interrupt extended keyword tells the compiler, among other things, to end the function with a RETI instead of just a RET - so this should be used as an ISR only.

You need to separate-out what needs to be done in the ISR from what needs to be done in the "main loop"