I figured out one reason for what causes this. By default whenever a new Discord server is created the notifications are set to notify for ‘All Messages’. Some server owners do not adjust this.

In my opinion, this is a pretty ridiculous idea. Not only will you get repeated notification sounds from all of the servers that use this setting, 99% of the messages will be irrelevant to you. It’s not uncommon to join many servers when using Discord. If multiple servers use this setting, you will get a lot of mysterious beeps.

To fix this:

Right click on your servers and check to ensure your notification settings are set to ‘Only @mentions’. You may also want to suppress the other notifications if it’s not a server you use often.

To replicate this issue, right click on a server and set the Notification settings to ‘All Messages‘, you will get the Discord message beeps but you won’t see a red icon for that chat channel. However as soon as you hear the beep you can look at these channels and see new messages for them. This is extremely confusing as there should be a Red Icon next to the channel indicating that a new message was received since it triggered a sound notification.

This is a really bad UX design pattern, imagine if you kept hearing your phone’s SMS sound go off but no notification showed up, I would throw that phone out the window.

This issue was reported 5 years ago with hundreds of comments but Discord still has yet to actually address it as seen here: https://support.discord.com/hc/en-us/community/posts/360042449511-discord-beeps-without-showing-where-the-new-activity-is