I have this problem too. "Greedy" Excel jumps in front of any other App. This is the case even if I have two windows of the one App on the two monitors, e.g. two Firefox windows.
So, you have two monitors, with App A having a window on each monitor.
On Monitor 1 you also have a window open with "greedy" App B (like Excel - I haven't noticed it with other Apps, but I wouldn't be surprised if it was a MS-endemic issue).
You are going between the two windows of App A, on the two monitors.
As soon as you click on the App A window on Monitor 2, greedy App B takes the front of the windows stack on Monitor 1, forcing you to click again on Monitor 1 to get focus in the window that you actually want to look at. But annoyingly, you didn't want to click at all on Monitor 1, since you're actually working on Monitor 2.