Weird Audio Probing

[NFX]

Has anyone found a signal using a probe and a tone generator only to find you can hear a tone through it but not in the guitar output if that makes sense.

A friend of mine made a phaser pedal, he couldn't get it working so he probed it, he said after the last component he could hear phasing in the tone generator but when he plugged the guitar straight in after the component he gets nothing. weird, i said ive never heard of this, any of you guys know?

[GibsonGM]

You sure he didn't just hear 'the tone' (from the generator) and not an actual 'phased tone'?   Or perhaps it was distorted and altered, but not actively phased..... If there was a feedback loop, perhaps the raw input was still able to bypass the active devices and make it to the output that way.   I've experienced that, and it can throw you....there is SOME path there. 

Edit: as said below, my answer assumes the switching is correct, as on a commercial pedal (usually). If the switching could be miswired, new build, see below...that ALWAYS needs to be checked first, or as I do - check the PCB before any switching is installed and then you'll know exactly what went wrong if it doesn't work after you do your 3PDT thing.

[Govmnt_Lacky]

3PDT output section wired wrong.
Output jack wired backwards (output on the sleeve, ground on the tip)
If they used a TRS output jack, wired the output to the ring.

Couple of explanations