When checking a topic that contains embedded content, Acrolinx IQ will flag any issues it finds inside the embedded content. While you are working in the container topic you can view the suggestions on the Acrolinx IQ shortcut menu but you cannot make corrections to the embedded content.
To make the corrections you'll need to open the embedded topic for editing. To do this, right-click anywhere within the embedded content and choose Open from the shortcut menu, or place the cursor inside the embedded content and double-click. When the topic is open, choose Check Topic from the Acrolinx IQ command group, then work through the flags and correct the issues. When you have finished the corrections save and close the topic.