They never thought it was a bomb
Ahmed Mohamed made a clock. No one except possibly his English teacher thought it was a bomb. The police never thought it was a bomb. They thought it was "a hoax bomb". That "broader explanation" the cops wanted? That was for him to admit he wanted to scare people by leaving it "under a car or in a bathroom". When he wouldn't back down from saying it was just a clock, that's when they arrested him. Because he's brown, he's named Mohamed, and his father is political, he therefore couldn't be a geek trying to impress people at his new school by building something, no; he had to be a troublemaker terrorist-wannabe out to terrify his school.
So it doesn't matter that they didn't evacuate the school or put the clock in the same car as themselves. They always knew it wasn't a bomb. But they thought he wanted people to think that, really, and that's why he brought it to the school.
I can't quite decide if that makes what they did worse or not. But it's not that they can't tell a bomb from a clock.