MOSFET LED Driver for low power LED's
Few things to check:


Are the grounds of the 12V and microcontroller supplies tied together? (they should be)
Is the MOSFET the right way round? (also the BJT)
Is the MOSFET gate floating at any point? (check wiring with multimeter for continuity between gate and uC pin)
As suggested by Bitrex, is there any oscillation?
Check the rest of wiring and also node voltages with multimeter to make sure things are as they should be - also make sure resistor values are correct


If you  still can't find the issue, can you post an image of your board layout (pics/gerber) and measured voltages if possible.