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 CtrlTab don't works 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 Win modifier are still working! Even the focus is inside child GUI application. By default, you may use WinQ and WinShiftQ to switch tabs. These hotkeys are defined on the "Keys & Macro" Settings page.
Goto "Keys & Macro" page, find row with "Set focus to ConEmu" description and choose hotkey, WinBackSpace for example. Please note, that some key-combos may not works - Windows capture many combos.
So, you may press WinBackSpace while keyboard focus is in Putty and after that CtrlTab must works. You may try this with notepad - keyboard focus will be more obvious.