Bacteria, due to a variety of reasons, have the ability to develop resistance to most anti-bacterial agents. So if a large enough sample of bacteria are taken, there will be a very very tiny fraction which are resistant. So when they say 99.9% of bacteria, they are acknowledging this fact.
Though different bacterial strains have varying capacities to develop resistance, I do not know of any specific strains which are resistant to disinfectants in general. Maybe a bacteriologist might offer her/his opinion.