When checking a topic that contains embedded content, <acrolinx> 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> 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> command group, then work through the flags and correct the issues. When you have finished the corrections save and close the topic.