Normally, rocket manufacturers show capability as "payload to LEO" or "payload to GTO". These aren't super-precise; LEO means roughly between 160 and 2000km altitude, which is a pretty broad range. If a rocket can deliver 13,000kg to the 400km altitude of the ISS, it can deliver slightly more than that to 200km, and slightly less than that to 2000km.
Weather conditions and manufacturing variations in individual rocket engines means there has to be a few percent of margin in the specified payload.
The flight control systems know their altitude, speed, and so on, and continually compensate for it; if the rocket is accelerating 0.1% less quickly than it's supposed to because of a 10kg stowaway, it may be able to compensate by firing the orbital insertion stage for a bit longer.
Because of uncertainties in the flight profile (weather, hardware variation, imperfect timing of engine cutoff) it's common for the actual orbit reached to be slightly different from the one intended. This is not a big deal in most cases, and if positioning is critical, the payload will have thrusters of its own to fine-tune its trajectory.
Once you're talking about a human-sized stowaway, that's about 1% of Falcon 9's payload. That would probably make enough difference that the mission controllers would actually notice, but I'd be shocked if there wasn't at least sufficient margin of fuel tankage to handle that -- I'd call it negligence otherwise.
Typically these rockets have an thrust-to-weight ratio at launch of 1.15 or above. For Falcon 9, you'd need 75 tons of additional payload to keep it from leaving the pad entirely. Even then, once you'd burned off some fuel, the rocket would conceivably fly -- except you'd destroy the launch pad first, and that would doubtless destroy the rocket as well.