Raising the ISO value only ever increases noise indirectly, due to the camera changing one of the other exposure parameters in order to compensate for the ISO setting you've chosen. What causes noise is not capturing enough light.
This is very important, as it means you can use auto-ISO in manual mode without any fear of increasing noise. Using the highest ISO setting the doesn't blow the highlights actually reduces noise compared to underexposing and having to boost exposure in post.
Using auto-ISO in Program, aperture priority or shutter priority can cause the camera to use a shutter-speed or aperture that will let less light in therefore increasing noise (and reducing dynamic range / tonal range).
However it's important to realise there are tradeoffs to be made, had the camera not increased shutter speed (and therefore captured less light, leading to more noise) as a result of using a higher ISO, then the image may well have suffered from motion blur.
Some of the images you captured in auto-ISO mode may have had more noise than if you had fixed the ISO at a certain value, but they would probably have suffered in other ways. These features were all implemented to make your photos better. If raising ISO actually generated noise, then everyone would shoot ISO100 all the time.