Your observation is interesting in that fava beans contain high levels of oxidants. Persons with genetic susceptibility can get very sick from eating them. This illness is called favism.
The problem is that the bean’s protein content can include as much as
2 percent vicine and convicine, which are converted in the gut to
divicine and isouramil. These highly redox proteins are likely to
retard rotting of the bean, but produce reactive oxygen species (ROS)
including the superoxide anion and hydrogen peroxide, which rapidly
oxidize NADPH and glutathione. These molecules are normally detoxified
by catalase and glutathione peroxidase, in enzymatic reactions that
depend on NADPH. Because NADPH levels are very low in G6PD-deficient
red cells, these undergo severe oxidative damage. A characteristic
feature of favism is that intracellular and extracellular hemolysis
Let us assume that color and flavor change described is due to these oxidants acting on the bean. How to prevent? I can think of one of 2 ways. 1: add antioxidants 2: prevent exposure to air.
The antioxidant that comes to mind would be lemon juice. The experiment is easy: a batch of fava beans, then treat half with lemon juice and the other leave alone. Does lemon juice prevent the color change? Lemon juice works to prevent browning of sliced apples by this mechanism.
The other method would be to exclude air. One could do this by tossing the fresh cooked beans with olive oil, which should produce an air barrier on each bean. Submerging beans in oil would be a surer way to achieve the same purpose. A third method would be to contain them in an airtight bag or container and exclude air first before sealing. Again, testable.
*Note that submerging cooked beans in oil is not a way to keep them indefinitely. Different and possibly more dangerous types of spoilage can happen. Both of the above ideas are to keep your beans good for a couple of days at most. Both sound delicious to me.