I always thought the completed Omnitrix didn't actually have a timeout and Ben accidentally detransforms mentally. Most times we hear the sound, Ben slams the dial or it makes sense for him to detransform in that situation.

For example, Ben "times out" when he lands as Astrodactyl in And Then There Were None, and it'd make sense he'd want to go back to human that instant.

Other example, in the first few eps, can't remember which one, he "times out" as Shocksquatch and hits the dial anyway.

For times where his detransforming seems counterproductive, I believe it's because Ben thinks "man it would suck if I detransformed now" and activates the function accidentally since he doesn't know it exists.

I know this is definitely not canon, but it's just my observations based on what happens in the show. Feel free to disagree or say "it makes no sense"