Let me guess ... the CU ran for longer than normal.

If this is the case look at the SQL errorlog and you will see a series of messages in the log indicating that so-and-so could not connect because the SQL Server was in 'single user' mode.

We recently ran into this situation when applying a CU to a normal SQL Server. We had to stop the SCOM and SEP services - they were connecting into the SQL instance when the CU process was trying to get in and execute scripts in the master database while the engine was in 'single user' mode.

SCOM and SEP may not be the only services, maybe 'Always On' is shooting you down as well.

Take heart though, once you find the culprit and terminate their access the CU will update normally.