Two slightly different focus problems, probably related. In both cases I can reproduced it with two split panels, starting with the cursor on the left side, focused gutter border also on the left:
1. Command Line
Click in command line or Ctrl Enter to command line. Then a single click into the right window:
Focused border remains on the left side. Cursor indicator appears in both windows. When typing characters they appear on the left side (although I tried to activate the right side).
Clicking again fixes it.
2. Console plugin
Click into Console command line (docked at the bottom). Then a single click into the right window:
Both gutter borders have the focus color. Everything else is correct: The Cursor indicator appears on the right side and when you type the characters appear also on the right side.
Clicking again removes the focus color from the left side.