Patching Linux in AWS

We are running an Ubuntu 14.04 kernel that is optimized to run in AWS. We recently ran into an issue where patches that were applied blew up all of the Linux instances and they had to be restored. We have been patching these servers for probably the last 6 months without issue. Does anyone have any insight as to what could be causing this? Sorry if this is vague, I have very little knowledge about Linux…