Its probably sensor dust. Dust/scratches on the rear element of a lens are a much bigger problem than on the front, but minor dust on any surface of the lens, even inside, is rarely a problem. The easy solution is to get a sensor cleaning kit, and some quality lens cleaning solution and cloth/tissue. Also get a lenspen or rocket blower. I give each lens element, and the inside of my lens caps a quick puff every time I change a lens. It really goes a long way keeping everything dust free.
As far as keeping UV filters on lenses...I used to keep High quality UV filters on lenses just for the protection, however, I found that uv filters were more difficult to clean than the lens itself, and were more prone to smearing, and collecting dust, and offer minor protection. Now I don't worry about some thin piece of glass for "protection," but I do keep a lens hood on my lenses all the time. Day, Night, indoors, or out, anytime, anywhere. A lens hood Is the best protection you can put on a lens.