I haven't used the repair program recently on a Win 10 machine but I've also had the getting Windows ready on shutdown on mine and it has lasted for about an hour.
Win 10 is constantly getting updates which you can see in reliability history, but the last getting Windows ready didn't show any updates, but you will get that message on shutdown whenever the machine is updating.
As to whether it is directly related to running the repair program, I cannot say, unless it is related to the apps reset.
Can you run the repair program again but uncheck all repairs for the apps and then see if you still get the message.
Win 10 is currently receiving the Fall update and Flash Player update, so you could get some disruption after the Flash Player update, but you'll know about the Fall update as it takes a while to download and install - and then there's the working on updates after the restart.
