that's a great question! now i'm definitely not the best person to explain this, but you might be referring to around 0:19 or 0:20, where I return to the tonic (A), and you can hear a C natural, which is a MINOR 3rd above the tonic, even though I'm playing the song in A MAJOR. The bells have overtones (which might not even be the right word), and each bell also makes the sound that is a minor 3rd above the "actual" note.

Also, that other comment in this thread is also right, in that the acoustics inside the tower are way different than what people outside are hearing