Madogre has a wonderful, insanely obsessive article on the guns used in The Matrix that describes even the guns used by minor supporting characters. Halfway through the article, the armorer for the movie breaks in to talk about exactly what it was Mouse was firing.
Mouse breaks out an odd pair of guns when the Agents cut the hard line after Neo sees the same cat twice. These guns are in a crate filled with .50BMG rounds... making some believe these guns are .50 calibers. This isn't true as that would be impossible.
Mouse's guns really were ... well, see the article.
(Image from Madogre)