A picture would help but it sounds like brown jelly disease, which can effect one coral or wipe out an entire tank.
below the line is not my writing but I hope it helps
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What we are talking about here, is bacterial disease. The brown filaments, or masses floating over and above a coral, are sure signs of it. They tend to develop slowly and then suddenly, one morning, there is a whole amount of it.
Often it is brownish and somewhat transparent. It can easily be mistaken for algae growing "on" the coral when it first starts. It is not.
Brown jelly disease, as it is sometimes called, is a very serious matter and, if not dealt with immediately will result in progressively more and more loss of tissue and eventually the loss of your coral.
One method we can implement to minimize damage to corals is to ensure that all of them receive good water current flow over their bodies (polyps) and that the flow is uneven. Laminar current is not really what you want.
Irregular water motion is better and cleans the coral better. This often prevents bacterial infections and the ensuing bacterial disease and the associated degradation of the coral from even starting.
Potential Causes
Corals are in an environment of real low water quality parameters:
High levels of total nitrate are often an indication that the water quality is low and may lead to the start of bacterial disease.
Total nitrate is calculated by taking the nitrogen-nitrate reading your test gave you, and multiplying that number by 4.4. Note that most tests on the market give results in N-NO3 and not in "total" nitrate. Normally the instructions that come with the test will say so. Some do not. If you are unsure about what your test really measures, you can always resort to calling the manufacturer.
When your N-NO3 level is high, e.g. between 60 and 80 ppm, your real nitrate level (total nitrate) is really between 260 and 350 ppm.
This is extremely high, and sure to endanger your corals and your fish as well. High phosphate levels may contribute to this too, as they will result in wild, and sometimes totally unexpected, growths of undesirable micro-algae. These can, and often do, grow on the corals skeleton(s) and may start affecting the polyp too if the growth continues. Remember that some algae give off toxins (releasing them on the coral polyp if that is where the algae growth is occuring).
High silicate and silicic acid levels (ppm) give rise to the appearance of diatoms (hobbyists refer to them as brown algae). This can affect the corals too and often does (see below).
The real danger lurks when encrusting diatoms start to grow on the skeleton of the coral, start moving upwards along the skeleton, reach the polyp, and start pushing the polyp out of the way.
When this happens, the polyp detaches from the exoskeleton and loose fringes of polyp are/may become visible. Sometimes these polyps die off and holes or bare patches on the skeleton (missing tentacles of the polyp) are clear evidence that this is what is going on.
