Let's go back to your example. A grad student has a minor pathogen escape incident, and it doesn't harm anyone. Faced with years in federal prison and the effective end of their future, do you think there is a chance they might not self report?
I'll give you another example. Lots of pilots have stopped self reporting mental illness because it is extremely punitive for them to do so (after incidents like Germanwings). So the metrics look better, and the actual problem has been swept under the rug.