If the effects of the tides are significant, and the spaceship inhabitants are observing the planet, it's likely that they would know that they are influencing the tides of the planet. However, if they're on some sort of commercial mission, rather than a "don't interfere/we come in peace" mission, it's highly likely that they may just not care. If that's the case, then there are numerous things that a spaceship could do that might affect the tides of the planet. Here are some examples:
The spaceship could be really big
A spaceship big enough to affect the tides would act like another moon, though tidal effects would be more variable/random if the spaceship was moving around. In this case, the spaceship would probably be visible from the planet, though cloaking fields etc. could negate this. Effects on the tides wouldn't come all at once, but rather would be a steady shift towards a new tidal equilibrium. Tides are a resonance phenomena, so it will take a few days/weeks for the tides to shift into the new pattern.
The spaceship could produce artificial gravity
Things like Alcubierre drives rely on warping space, which would likely affect the tides. Since this would be a less constant effect, it would probably cause something more like a tidal wave than a consistent change in tides. There would be a consistent effect if the spacecraft was using artificial gravity to stay at a certain non-natural orbit. For example, if a spacecraft wanted to be in a geosynchronous orbit, but at a low altitude, the craft could do this by reducing the effect of gravity from the planet on the ship. If this reduction in gravity affected the ocean under the planet, it would cause tidal effects.
The spacecraft might need to either dump things into the ocean or suck up water
A huge craft spending a few days/weeks replenishing internal water supplies by sucking up water would definitely cause tidal effects if it was using something like a gravitational tractor beam to do so. Likewise, a spaceship dumping all of its garbage would cause huge tidal waves. If they were cleaning out some internal holds by sucking up and dumping water repeatedly, this could cause alternating super low tides and tidal waves, along with massively disrupting currents on the planet.
All of these things would be very noticeable for the people in the spaceship, but they might not care. They may also not be paying any attention to the significance of changing the tides on the planet for the people below. Consider the effects of oil prospecting in the rain forest on the natives living there. The prospectors aren't really unaware of what their presence does, but they don'r necessarily think or care about the consequences. I could definitely see a space faring nation having similar attitudes towards a pre-industrial culture.