Generally simulating a key which is a hot key leads to unpredictable results, since the simulated key may either trigger the macro or go through to the application. Keyboard Maestro tries to make it the latter, but because the keyboard event queue is an asynchronous queue (ie, the system may take an arbitrary long time to process the simulated key), there is no way to guarantee it.
You can explicitly disable the macro, simulate the key, pause for some length of time, and then re-enable the macro. If you know you won't want to trigger the macro again for several seconds, then you can safely pause for quite a long time which should ensure the system has had a chance to process the key.