I have found out that if I clean copper with clad mine are like that too so I clean all my copper by itself and it doesn't do that,nickels will turn red also if cleaned with clad,try doing them seperate.
It's a normal rust on some pennies, especially from the WW2 era. The composition was changed and I think they used spent cartridges in the making?? If they are common coins, try heating up some hydrogen peroxide in a shot glass for about 15 seconds and drop that penny in and watch it fizz. I think the red will be gone lol If you want to see it slower, heat up the peroxide and use a Q tip and rub it on, over and over.