LT3680 switcher output doesn't have regulation under no load
The problem is very likely to be loop compensation.

This is a current mode architecture, so the output pole changes with load, but the output zero does not.

The output pole is at \$\frac {1} {2 \pi\ R_o C_o}\$; rearranging as \$R_o = \frac {V_o} {I_o}\$ we get:

\$f_p = \frac {I_o}  {2 \pi V_o C_o}\$

At very low load currents, the output pole is at a very low frequency and when added to the dominant pole at the \$V_c\$ pin, the arrangement could easily be unstable.

Positive feedback could indeed make Vo = Vi.

To cure this, you could add a capacitor (need to calculate it) from \$V_c\$ to ground and add a small (100pF perhaps) capacitor across R46

Another point to note is that for low load currents, the size of the inductor is very small (as load current increases the required inductance value decreases). 

The inductor in the application circuit has been chosen for about 1A of ripple current; if you have only a few mA of load, then I calculate the inductor should be of the order 120μH assuming a maximum load of 100mA (for a ripple current of 40mA).

The datasheet gives guidance on this

\$ L = \left (\frac {V_O + V_D} {F_{sw} \cdot \Delta I_L} \right) \cdot \left ( 1 - \frac {V_O + V_D} {V_{in(max)}} \right)\$

See page 10 of the datasheet.