I would suggest storing the enemies in an array, and then placing that array under the enemies
key in the dictionary:
var enemies_array = []
for e in get_tree().get_root().get_node("MainScene2D").get_node("Enemy A").get_children():
enemies_array.append(e.get_name())
# Store the array in a dictionary:
save_dictionary["enemies"] = enemies_array
Another way you can do it is by using a for loop, though it will be harder to use than an array:
var enemies_dictionary = {}
var enemies_to_loop_through = get_tree().get_root().get_node("MainScene2D").get_node("Enemy A").get_children()
for i in range(0, enemies_to_loop_through.size()):
enemies_dictionary["Enemy_" + str(i)] = enemies_to_loop_through[i].get_name()