If you're using canned baked beans your best bet is to rinse them off.
Sort and rinse the beans. Discard any beans that are shriveled or cracked. Add the beans to a large pot and cover them with water. The pot needs to be big enough to allow the dried beans to expand three times their size. You will need 6 to 8 cups of water per pound of dried pinto beans. Boil for the water three minutes and remove the pan from the heat. Cover the pot and allow the beans to sit for 1 to 4 hours, depending on how much time you have. One hour is enough time for the beans to soak, but more time can reduce how much gas the beans produce. Discard the soaking water. Rinse the beans one more time and then proceed to cook them as normal.
Soaking them too long, probably.
When cooking rice and beans together, a combination of spices (onions, garlic, green pepper, tomato paste, olives and other spices) are saute, the beans with the water they had been soaking in are then put in and finally the rice if it needs more water it is added. So yes one will say that the rice is boiled in it. On the other hand you don't want the beans to soak for too long (12-24 hours the most), if they do it will be best to dispose of it rinse the beans and cook with new water.
Although some sites don't tell you to do so, soaking beans overnight is best done under refrigeration for food safety purposes. Dry beans are an agricultural product and have had plenty of exposure to critters, soil and irrigation water which could all contribute to a population of unknown micro-flora. Hydrating the beans at room temperature for an overnight will allow the growth of any pathogens that are present. The bacterial load will be increased and any toxins produced might not be destroyed when the beans are cooked. So, to avoid dealing with all of that, soak the beans under refrigeration.
Rinse them off and re-season.
Soaking them on the counter at room temperature is the smartest.
Yes, it does not affect anything.
Soaking pinto beans before you cook them speeds up cookign time and allows some of the gas to escape. When soaking beans the water should be change the water several time, or when it begins to turn dark.
Traditionally beans are soaked to lessen the amount of time it takes to cook them. Unsoaked beans merely have to be cooked longer to desired tenderness (usually an hour longer).
Many times foreign mater such as dirt and small stones may be present, I also like to remove any undesirable looking or damaged peas. The soaking process reduces the gas forming properties of the beans. Be sure to discard the soaking water and cook peas in fresh water. Enjoy!
it rehydrates them. this MAY loosen the cellulose layer, wich aids in digestion