Im confused. Did you let the car sit at your shop for 2 days and came back to it and found the water in the intercooler, or did you drive the car? If you drove the car with the kit installed, it all comes down to a solenoid, or the lack of one. The vacuum in the charge piping can siphon liquid through the lines. Its a good idea to install a solenoid just before the nozzle so that cant happen. You wire the solenoid to come on when the pump comes on, and it allows fluid to flow through it and to the nozzle. When the pump turns off, the solenoid turns off and does not allow any fluid to flow past it.
Hope this helps.