Looks like a typical phosphoric acid based material reaction. It could be that in the areas that are rusting already the material was used too sparingly or without allowing sufficient reaction time. If it were me I'd go back over the rusted spots with the rust conversion material by hand (gloved of course) as a touch up. Then if you had any doubts about the success of the conversion process spray a coat of etch primer before topping with epoxy primer. If you're good with the conversion process then go straight to the epoxy primer/sealer.