When we went to OmniFocus 2 we had this same issue happen where when you mark repeating tasks as complete it then highlights the repeating tasks which throw off where you are working. For me, it is even worse because I delete the task so it is not part of my history since it is a way to track what I actually did that day. Now I have to reselect all my actions again that I selected and then go back and delete them and my macro of the spacebar to mark as complete and then delete to remove the task no longer works. I removed several tasks before I realized what it was doing just because it is so habitual.
To make matters worse if you have different actions highlighted and one is repeating and one is not and press spacebar you can end up with selections all over the place depending on how it is grouped and not even realized the new action is still highlighted much lower. By pressing spacebar again to uncheck actions as complete you are now marking actions that remained highlighted that were complete as not complete and the newly highlighted action that isn’t complete as complete, what a mess and you likely will not even realize that happened!
To make matters worse there is no perspective option to filter by repeating actions.