Amazon offers some excellent cloud computing services, but being self-managed at the basic level it can be a headache to diagnose and fix errors. I recently encountered a similar error where all my attempts to login into the EC2 instance failed with
cloud-init: runcmd Caught exception reading instance data: http://169.254.169.254/2009-04-04/meta-data/security-groups as shown in the Amazon EC2 instance console system log below.
While there is no information or solution available, it seems this error is related to some sort of communication/hardware node failure which hosts the security meta-data policy - failing to read which no connections are allowed by the instance.
A temporary solution which worked for me was to the affected instance, things worked perfectly after I rebooted my instance.