In recent months I've found Teams chat notifications are inconsistent. Sometimes the popup will appear every time and make the notification sound, other times messages silently appear even if you don't have the chat open on your screen.
This is leading to all kinds of missed messages because the only way to keep on top of it is to look at the icon in your taskbar. It happens with several of our users, it's happening to me both on my work desktop and home laptop so it's not the local computer that is at fault here. Notifications are all on and default, nothing has been changed on our admin portal policy wise.
This wouldn't be too bad except in my case I've noticed some messages are being marked as read when I clearly never heard any notifcation noise or popup.
The only thing I can come up with is that they tried to turn off notifications when your teams chat list is open, to minimize the amount of noise. However it's happening when the window is minimized or out of focus which is not helpful at all. I just want an option to keep ALL chat notifications on. If I want focus assist I'll let windows take care of it.
If it's not only affecting you and your device but many users you know it's something else that standard troubleshooting won't solve. I suggest you reach out to Microsoft with an official support ticket.