The bike is a 2010 Ex250. I'm assuming this could be damage because I have laid the bike down towards the shifter side more than once. Damage that could have transferred to what I see now. Also, I have tried to split the crankcase without taking out the clutch basket (stupid me) that might have put undue stress on the parts mentioned.
You and concours are right in that there IS a plate/disc that keeps these apart and in normal operation, there is 0.00001% chance of these two coming undone from their places and hooking up like in 3rd picture. I am just worried about the loosness.
All in all, I see no damage to the riveted area that would lead me to believe that they could have gotten that way because my mistake while trying to split the case.