KM freezes after 'confirmation window' pops out

KM freezes after confirmation window pops out.
As you can see the top right part of the picture, KM freezes.
The only way to unfreeze the KM is to click 'close button on confirmation window by myself. (not works with KM keystroke function. not works with KM quit safari function)

What shoud I do to avoid the freezing ?

furthermore , hardware keyboard freezes when KM freezes...

Certain actions can be synchronous when they aren't expected to be. The most obvious one if the Press a Button action - generally the API immediately returns from a Press a Button accessibility command, but for certain applications, the API will not return until the application finishes processing the behaviour induced by clicking the button which will lock the Keyboard Maestro Engine up until that time.

There may be other cases, but without knowing which action is actually in progress at the time it's hard to say. The Macro Debugger user manual section might help pinpoint the action.