Ionization disturbances were disturbances in the ion field of a planet, for example.
In 2366, a class-1 probe detected ionization disturbances on Nelvana III. It was suspected that the Romulans had built a base on the planet, the disturbances being one sign pointing towards that. It later turned out that they were created by a cloaked orbital probe used by the Romulans to study the planet for archaeological research. (TNG: "The Defector")
Cloaking fields leave behind ionization traces. As the planet Meridian didn't create any such disturbances as it appeared out of nothing, the crew of the USS Defiant was able to determine that the planet had not been cloaked. (DS9: "Meridian")