• iTerm2 version: 3.2.7

So, say, you've invoked Hotkey and now want to switch to normal iTerm2 window(s) you have running cutting the corners: not hiding it back with same invocation shortcut.

Before activating Hotkey Window, though, iTerm2 wasn't focused (you have other apps windows there).

Now when you pressed that switching shortcut (Alt-~), iTerm2's next window is being chosen right indeed, but it isn't focused — but previously focused other app's window is.