Microwave energy is absorbed primarily by water in the food.
The waterlogged canned peas and their surrounding liquid absorb microwaves at pretty much the same rate and will therefore get hot more or less equally. When the water begins to boil, the peas are at about the same temperature, whereupon you undoubtedly consider them to be done and stop the oven.
The much drier fresh peas, on the other hand, don’t absorb microwaves as readily as the surrounding water does, so the water heats faster. But the relatively cool peas prevent the water from being heated uniformly.
At the same time, the peas are acting as bubble instigators (Techspeak: nucleation sites), encouraging the water to erupt exuberantly wherever there are hot spots. All this happens before the peas are adequately cooked and you deem them ready to remove from the oven.
Try using a less-than-full-power setting, in which the oven zaps the food on an intermittent schedule, giving the water time to distribute its heat through the peas. That way, they’ll be cooked before the water has a chance to boil over.
Better yet, buy frozen peas. The producer has tested the best way to cook them in a microwave oven and the directions are right there on the package.