It's just a trick. The methodology used to arrive at >100% numbers doesn't actually consider all of the caloric energy in the fuel. The difference between higher and lower heating value of methane is about 10% and condensing boilers are usually marketed as 107% efficient.

The gist of it is that the fuel might contain 1 kWh of chemical energy but 0.1 kWh was traditionally lost to water vaporization during combustion, so they start with a denominator of 0.9kWh and since condensing boilers capture this "lost" energy through condensation it leaves you with >100% efficiency, on a technicality. No laws of physics are being violated.