To get a full answer you should really get in touch with the owner of the app, because it does really depend on how their track is constructed and how they intend it to work. I have one 50-minute sleep track which takes you down into delta (http://www.mindamend.com/shop/sleeping-and-dreaming/sleep-induction-isochronic-tones/) and that is designed to just get you to sleep, so you just let play until the end. If you played that track on repeat it might make you jump and wake you up, as the track begins at a higher frequency. I have another 8-hour sleep track which is meant to be played all throughout the night (http://www.mindamend.com/shop/sleeping-and-dreaming/deep-sleep-8-hour-sleep-cycle/). So it does depend on the individual track you are using.
It may be that you had the volume too loud, but I would expect you to hear the effects of that straight after you’ve stopped listening, not on a day you haven’t used them. It might be something similar to muscle memory, where you suddenly remembered the sound and sensations it gives you as if you were hearing it again. I don’t know how long you’ve been using this type of thing for, but maybe it’s something that will settle down and disappear once you become more accustomed to the sound.
Binaural beats can easily be heard at the low frequencies (< 30 Hz) that are characteristic of the EEG spectrum (Oster, 1973). This perceptual phenomenon of binaural beating and the objective measurement of the frequency-following response (Hink, Kodera, Yamada, Kaga, & Suzuki, 1980) suggest conditions which facilitate entrainment of brain waves and altered states of consciousness. There have been numerous anecdotal reports and a growing number of research efforts reporting changes in consciousness associated with binaural-beats. "The subjective effect of listening to binaural beats may be relaxing or stimulating, depending on the frequency of the binaural-beat stimulation" (Owens & Atwater, 1995). Binaural beats in the delta (1 to 4 Hz) and theta (4 to 8 Hz) ranges have been associated with reports of relaxed, meditative, and creative states (Hiew, 1995), and used as an aid to falling asleep. Binaural beats in the alpha frequencies (8 to 12 Hz) have increased alpha brain waves (Foster, 1990) and binaural beats in the beta frequencies (typically 16 to 24 Hz) have been associated with reports of increased concentration or alertness (Monroe, 1985) and improved memory (Kennerly, 1994).
Binaural beats are auditory brainstem responses which originate in the superior olivary nucleus of each hemisphere. They result from the interaction of two different auditory impulses, originating in opposite ears, below 1000 Hz and which differ in frequency between one and 30 Hz (Oster, 1973).For example, if a pure tone of 400 Hz is presented to the right ear and a pure tone of 410 Hz is presented simultaneously to the left ear, an amplitude modulated standing wave of 10 Hz, the difference between the two tones, is experienced as the two wave forms mesh in and out of phase within the superior olivary nuclei. This binaural beat is not heard in the ordinary sense of the word (the human range of hearing is from 20-20,000 Hz). It is perceived as an auditory beat and theoretically can be used to entrain specific neural rhythms through the frequency-following response (FFR)--the tendency for cortical potentials to entrain to or resonate at the frequency of an external stimulus. Thus, it is theoretically possible to utilize a specific binaural-beat frequency as a consciousness management technique to entrain a specific cortical rhythm.  
♥ I've beeen training in self-hypnosis for a while (under supervision and for a reason) and found that the 8-4 Hz beats put me very quickly in a deeply relaxed state. Definitely the thing! With the timer, I can shut them for the real self-hypnosis. I haven't tried the other beat generators yet, but this one works much better than I expected and clearly does the job. In a few words: I'm impressed!
The activity of neurons generate electric currents; and the synchronous action of neural ensembles in the cerebral cortex, comprising large numbers of neurons, produce macroscopic oscillations. These phenomena can be monitored and graphically documented by an electroencephalogram (EEG). The electroencephalographic representations of those oscillations are typically denoted by the term 'brainwaves' in common parlance.[4][5]
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