The most common phrase in german phrase book for apology would be es tut mir leid or tut mir leid to mean "it does me suffering". From the questions on the difference between "entschuldigen" or ...
Are there any well-known German expressions for someone who is very board and detailed in knowledge? for example: He is a human database
As I read here: The first two sentences are classified as "Nicht-Verstehen signalisieren". Are there other widely known terms or interjections to signal you didn't understand something?