The authors present scanning tunneling microscopy images and mass spectra that show that dosing gases at pressures in the range of 10(-6) Torr in an ion-pumped ultrahigh vacuum (UHV) chamber results in a measurable concentration of reactive molecular radicals and atomic hydrogen ions being created. One source of radicals is the fragmentation of the dosed molecule, while another is atomic hydrogen that is re-emitted from the ion pump itself. The dosing of noble gases such as helium also results in harmful radicals escaping the ion pump. These radicals are able to create new reactive sites on a hydrogen-terminated Si(100) surface; they show that these new dangling bonds result in extra molecular line growth in a 2,3-dimethyl-1,3-butadiene dosing experiment. These results serve as a cautionary note to experimenters working with ion-pumped UHV systems and surfaces that are sensitive to radicals, such as hydrogen-terminated Si.