As far as I understand it... brown jelly is caused first from trauma to the tissue of the coral. Either from a fish/invert or from handling. Once the tissue injury is there, the infection results when/if tiny little protozoans can get to it before the damage heals. Once the protozoan infects, it can spread quickly and digest the tissue. The protozoans also excrete some sort of digestive enzyme, which is why the jelly can spread to other parts of the coral, or other corals, and damage those as well.
Remedies... I've heard simply taking it out and brushing off the jelly may work, some people do FW
dips or lugols dips as well.
Preventative maintence... don't have coral nippers in your tank and secure all corals well so they don't fall or get bumped into?
Hope this helps.
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