It glitched again, but I saw what happened this time: the cat hit one of those round warp things just as it fell off the bottom of the screen. So the focus went down but the cat kept going. The score and milk gauge even ticked up sometimes!
Glad you like the game! Also, thanks for all the feedback and thanks for delving into this bug for me, saves me some time. I'll try and fix it before submission period ends.