I did the [Stable Update] 2024-05-29 yesterday and noticed afterwards that with GNOME 46.2 the windows counter indicators in the GNOME Dash to Dock extension (92-1) are displayed on top of the icons now.
Did a little bit of research and found it’s already been reported in Github:
A quick fix/workaround is to open the settings for the Dash-to-dock extension, open the ‘Appearance’ tab and change the setting for “Customize windows counter indicators” in the drop down from ‘Default’ to ‘Dots’.