Control stays with previous app after four-finger swipe?

On my mac (Sierra, OS 10.12.6), I have it set so that I can swipe between different desktop screens with four fingers on the trackpad. But when I do this, the "control" stays with the app that was in use on the previous screen.

I.e., if I am using the Messages app, but then four-finger swipe to change to the screen where Google Chrome is open, and then I start typing, the text is entered into a conversation in Messages (only noticeable after scrolling back to the previous screen), not into Chrome.

Is there a setting that can change this behavior? It is always counterintuitive to have the app that's visible on my current desktop not actually be the one I'm controlling.

EDIT

I just found that this issue occurs consistently when switching between screens with Messages and Chrome, but doesn't seem to happen for all apps. E.g., when I switch between screens with Notes and Chrome, the control switches to the new app as desired.

This is unexpected behaviour. There is no setting for this. Does this also happen when you switch to a different virtual desktop with the keyboard shortcut ctrl + left/right arrow key?

I would usually tell people to trash the plist that holds any related settings but it seems that com.apple.desktop.plist doesn't exist anymore in Sierra.

Installing sierra over the current install could mend your issue. Best to have the latest installer for sierra in that case and not an older version than you already have installed. This will, by the way, not delete you stuff. It will install the OS over whatever is already there. You can only loose stuff if you go erase the disk first before installing. Talking about re-installing, can you not install a later version of OSX? Maybe High sierra?