Most of the issues I've heard of where freshwater fish carried disease over to marine aquariums were related to the "freshwater" fish being housed under brackish conditions (or at least some salt). 4 ppt is enough salt for Amyloodinium (velvet) to survive, as well as some flukes.
@GlassMunky mentioned Lymphocystis - that could be possible, but only a few freshwater species get that (glassfish for example, a marine derived species).
Internal parasites of course easily go between freshwater and marine fish (since internally, they have the same osmotic balance) but in most cases, they are transmitted through predation.
Bacteria are a wild card - many species survive transferring from freshwater to marine (we backwash our filters with city water and the bacteria lives just fine). However, most bacteria are ubiquitous, and are found in all systems eventually.