Think of a guitar string. If you play a note and then slide your finger up the frets, the pitch gets higher as the string gets shorter.

Same thing is happening in the glass. The sound you’re hearing is the air in the cup vibrating and resonating. As it fills, that column of air gets smaller and smaller, like a trombone player pulling the slide in.

As the air column gets smaller, the length of the sound waves gets shorter too which results in a higher pitch.