50% CPU usage on MySQL RDS instance (db.m3.medium) with 0 connections
A possible reason:

The "Change buffer" queues up index changes for eventual writing to disk.  If you did a lot of INSERTs/UPDATEs/DELETEs on table(s) with non-unique indexes, the CPU could have been busy for some time after the queries "finished".

The reboot may have only coincidentally cleared up the CPU.  The change-buffer work must be done eventually, even after a reboot.