Recently, the folder icon changed and now it looks like a placeholder for unloaded content. I vote for removing it completely and only have favicons for actual websites. This would also save a lot of space in the browser bar.
Feel free to voice your opinion in the Github issue below.
There is an official response regarding the bookmarks icon:
Hi all, Brave product design team here. Thanks for all the feedback so far! We hear you and are working on a fix. It’s important to us that we have a bookmark folder icon that works for everyone, and clearly some considerations were missed in the initial update. Please be patient as we get a fix into the queue.