When you run or attach any GUI application in ConEmu tabs – all keyboard input (read focus) passed to this child GUI application.
That's why Ctrl+Tab doesn't work in your case – it is processed by PuTTY but not ConEmu.
But there is a way.
If you have enabled option "Install keyboard hooks" on "Controls" settings page, hotkeys with the Win modifier are still working! Even the focus is inside child GUI application. By default you may use Win+Q and Win+Shift+Q to switch tabs. These hotkeys are defined on the "Keys & Macro" Settings page.
Go to "Keys & Macro" page, find row with "Set focus to ConEmu" description and choose hotkey, Win+BackSpace for example. Please note that some key-combos may not work – Windows captures many combos.
So you can press Win+BackSpace while keyboard focus is in PuTTY and after that Ctrl+Tab must work. You can try this with Notepad – keyboard focus will be more obvious.