Sometimes when I'm editing sound files, or mixing music together in an audio program, you need to adjust certain things such as the volume of certain frequencies (using an equalizer).

This has happened maybe two or three times over several years: I will open the equalizer and listen to the music, and make adjustments to the equalizer. In my head, I am actually hearing the changes in the sound. After about 20 seconds, I realize what I'm doing isn't really affecting the music enough, and then it occurs to me. I am changing the equalizer on a track that is muted, and not the music that I'm currently playing back.

So even though I wasn't actually changing anything in the mix, because I believed I was doing it at the time, somehow I tricked myself into actually hearing that change even though it didn't happen.

I'm going to agree with Insom's hypothesis though. But, it is possible that the pen was dry (or needed a few seconds to get going), you wrote down without perceiving the lack of ink because you expected to just operate anyway, your mind wrote it out for you to compensate, and by the time you got back to review it, you noticed there was no ink.