Which is the phototransistor in Lesson 11 Evil Genius?
This is what I would do to test it. 

First, double check polarity of all components and disconnect all other circuits on the board. Then, remove the red LED and use your phone camera to check if the IR is on or off (cameras usually catch IR light), and disconnect the green LED before testing again (to avoid a possible feedback loop). If you can remove the green LED completely and test the voltage with a multimeter, that would be even better.

If this still doesn't work, try covering the npn completely, maybe with paper and black electric tape. And check to make sure your supply voltage isn't too high. If you cover the npn and it still doesn't work as it should, then you probably have a component with different functionality or your component got fried and fused inside, creating a short within the component.