Based on this thread, it appears that stack deletion can be problematic if the stack is altered.
https://forums.aws.amazon.com/thread.jspa?threadID=71050&start=0&tstart=0
Looks like you need to go via Support to get it deleted.
That said, I have been able to delete stacks where I have manually altered the components. Sometimes you need to wait a couple of hours after you terminate instances, VPCs, subnets etc before the stack deletion actually succeeds.