Hello
In general, PWM ICs have internal dead-time generation, which is what the minimum allowed DC reference to give the minimum duty-cycle is called. These things should be specified within their data-sheets. If you have built your own PWM generator with discrete components, then you should introduce a minimum DC level to forbid the comparator outputting continuously high-state that would possibly permanently damage the switch. Do note, though, that some ICs allow 0% duty-cycle, but that is also specified in their data-sheets and if it is so it's because there may be some special requirements to do so.
At any rate, if your application can't handle less than a minimum duty-cycle, then you should provide it.
Vlad