This question comes up quite often in some industries or where we havent sized the equipment for the customer.
The fundimental frequency is always directly proportional to the speed of the engine. If you fidn that the frequency is low, while the engine speed remains constant, the effect is caused by harmonic distortion. Harmonic currents are caused by non-linear loads connected to the distribution system. A load is said to be non-linear when the current it draws does not have the same waveform as the supply voltage. The flow of harmonic currents through system impedances in turn creates voltage harmonics, which distort the supply voltage. You can read more about harmonic distortion here.
Why is it happening? it doesnt happen on the mains!
The mains is a huge beast comapred to even the largest geenrator - you also don't have the same protections on the mains as you do on a generator. Harmonic distortion can be countered however there are three key ways:
You should note however that harmonics cause additional current to flow through the windings of the alternator and therefore additional heating occours. For this reason you should primaily tackle the harmonics if possible to reduce them to an acceptable level. If you have harmonics of significant quantities in the system, you will need to oversize he generator to ensure you are running within limits.
1) Oversize the generator
Oversizing the generator (specifically the alternator, rather than the engine) will reduce the harmonics as the THD as a percentage will be less compared to the overall power produced by the alternator.
2) Add some more resistive load
Resistive loads act as a 'break' on the harmonics, coutering their effects in the system and therefore adding additional resistive load can counter the problem of harmonics within a generator system (assuming you have suffiecient capacity to add these loads).
3) Monitor from the Speed, Not the frequency
You may turn off the frequency monitoring, if you have another way of monitoring the speed of the engine. As speed is always proportional to the fundimental frequency, your fundimental frequncy will not be low if your engine speed doesnt fall.
Most generators of standard design not using CANBUS to comunicate with the engine calculate speed from the alternator frequency. in this case adding a magnetic pickup to the system will allow monitoring of engine speed.