When using Acrolinx for MadCap Flare sidebar edition, if you replace suggestions from the sidebar, Acrolinx corrects the issues for you automatically. After Acrolinx updates your document, you might notice some empty selection tags where Acrolinx made the changes to your document. Though you see the tags, they're not really stuck in your document but rather a rendering problem in Flare.
Switching from XML Editor view to Text view and then back to XML Editor view will remove this visual issue. This refreshes the rendered document and the empty tags will disappear.