In MonoBook the notification icons are black because the apex theme does not support inverted icons. It should be possible to make them white, but last time they were flashing (T111821: Echo flyout icon flashes color change from white to black in MonoBook skin)
Related to this, there is a proposal for changing the notification badges which do not require inverted icons: T115845
The proposed approach worked well in our research sessions, but we have not checked if there would be some Monobook-related limitation. Feel free to comment on the ticket if you think there may be any.
A problem in the Modern skin has been reported: https://en.wikipedia.org/wiki/Wikipedia:Village_pump_%28technical%29#Notification_look_change
Based upon timing, it might be related to this. Does anyone know whether Modern uses the same Notification icons as Monobook?