When I was playing a couple hours ago, a small band of 5-10 storm cloaks attack the city of Whiterun. Only 3 made it to Dragonreach but one fell inside. and the final two killed the final guard inside, and I waited for a few hours and they just left. I joined the imperial legion and defeated Ulfric. Is this normal? I have encountered only a few Storm Cloak couriers in my travels of exploration. Is this a bug?

its just a way to show you that the stormcloaks were thechoice you shoulda made but, yes its a glitch (i assume)

Are you on PC or console?

This was probably just a random encounter.