The cause of this issue was found to be due to a recent code bug, a recent upgrade to the container orchestration service on the VMs hosting web apps caused an issue with disposing of old containers during recycling. This meant that sometimes, old containers weren't properly removed. The issue has been fixed and applied globally as of August 27th, and immediately caused duplicate containers to stop spawning.
If you have already scaled your plan up and down to mitigate the issue, the same problem should not happen again.