Is the denial of a specific act—believing it to be from the religion, then discovering it is not—considered disbelief (kufr), a whisper (waswasah), or a sin short of disbelief?

Perhaps the questioner is referring to the method of wetting the ear with water during ghusl (definition) without introducing it into its inner part, as mentioned by the jurists, such as Ibn Hajar al-Haytami, al-Bujayrimi, and al-Nafrawi. The correct method is to tilt the head and place the ear on a cupped hand full of water or pour water over the head without pouring it directly into the ear, for fear of harm. What afflicted you may be due to a misunderstanding or a wrong application, such as excessive rubbing of the ear or pouring water into it.

The aforementioned method is not obligatory. What is obligatory in ghusl from janabah (definition) is to generalize the water, and a strong presumption is sufficient. What happened does not entail sin or disbelief. It seems you have obsessive thoughts, and you must strive against them.