Thank you - well pointed out!
I found the same problem with the 2.5mm nut driver in my, non-iFixit, precision set. The nut is too shallow to engage with the hex socket because of the shape of the rounded edges at the mouth of the socket. Managed to overcome this by carefully re-engineering the socket with a diamond flat file ie filing it to remove the rounded edge and leave the hex opening flat and square. Worked perfectly after this.