I answered a question on Super User and while on other sites I did not get a 'Reputation Notification' to explain that I was given 2 upvotes for my answer - yet if I manually check my Profile here at meta.SE my total Reputation is in agreement with the amount there.
I'm not knowledgeable about the intercommunication between the servers and sites but I would explain it this way: Super User either failed to send or other sites failed to receive the message the I had a reputation update on Super User.
I should have received either two green star trophies (🏆) of 10 reputation each or one of 20; depending on when I returned to one of the Stack Exchange / Stack Overflow / Super User / etc. sites.
Here's a screenshot showing no reputation change notification for Super User:
Here's a screenshot of my Profile over at Super User showing that I was silently credited:
I'm bringing this up on Meta.SE in case the communication is broken between more sites than just Super User and everywhere else.