Bubbles appear when I take photos in the dark?

I use a Nikon D3100, anyone know why these bubbles appear?

Bubbles? Are you talking about lens flares, perhaps? Or maybe even bokeh?

Please link us to an example so we can understand your question better.

Because you're pop flash is reflecting back at you and lighting up the dust and grime. Like how your computer becomes a mirror in the wrong lighting situation.