The principal issue is the Scarborough Shoal/Huangyan Island which the PRC-PLAN took from the Republic of the Philippines by military force resulting in the Philippines being excluded from fishing in the area. How was this done? Well while the PRC was building a competent military structure the Philippines was doing nothing. While the PRC developed PLAN the Philippines was busy electing a disturbed and addled former actor and other perhaps not top level politicians to lead their Nation. In spite of having numerous shipyards to build a Navy and Coast Guard as the PRC has done they got some old ships which were not sunk as fishing and diving reefs and used them instead. As one might expect the training and capabilities of the crews manning these vessels is in line with the vessels capabilities themselves - no doubt they do their best. With one shot the PRC-PLAN could blow anyone of them out of the water and existence. Everybody knows this and it is pointless for the national pride of the Philippines, which is enormous, to believe something different.
It was clear from the start that no Nation around the perimiter of the South China Sea was going to stand up for their Territorial Rights against the moves and claims of the PRC so the only hope was to negotiate for some Rights, in the case of the Philippines fishing Rights around and near the Scarborough Shoal/Huangyan Island particularly since their general economy is tied in with that of the PRC. But no national pride, that block to clear thinking in the Republic of the Philippines, got in the way and as a result of their massive diplomatic faux pas they now have nothing.
What do the Republic of the Philippines do but make matters worse by running to the United Nations chanting - UNCLOS, UNCLOS, UNCLOS.
What has happened already is that Ma Keqing the PRC Ambassador to the Republic of the Philippines has told Foreign Secretary del Rosario that the PRC will address the issue through one-on-one negotiations and further that,
"China has indisputable sovereignty over the islands in the South China Sea and its adjacent water."
Even if by some extraordinary decision the UNCLOS should Rule, in four or five years time, in the favour of the Republic of the Philippines it is a non-binding arbitration and the PRC has not the slightest intention of paying any attention to such a Ruling.