1 exception(s):
Exception #0 (Magento\Framework\Exception\NoSuchEntityException): No such entity.
Exception #0 (Magento\Framework\Exception\NoSuchEntityException): No such entity.
How can multiple websites use same store? Could you please provide full configuration of your stores?
See screenshot below. I have added 4 websites that all use the same store.

Stores just have same name but ids would be different. Need more information to reproduce. How many root categories do you use?
I use three different root categories. Every Store has his own root categorie. The websites, stores and categories are created in version 2.1.1
Just came across this as well. 2.1.2
In 2.1.3 there is no error after deleting but in table "_store" and "_store_group" I have still records pointing to the website and view I have deleted. I noticed weird behavior when I added a category because the rewrite module added records with an empty store. Is it save to just delete the records in the two tables?
Problem still occurs in version 2.1.5 Does nobody else have the same problem. Can't be I am the only one here. Which info do you need more to investigate?
Still not solved in version 2.1.6, would be nice if it would be investigated or could some one tell me in which tables I need to delete records manually?
Why is this problem ignored. The result is corrupt data in some tables and could give big problems in the future. You should check the delete action for web site.
@GuidoHub, It's not like _this_ specific issue is ignored. Processing GitHub issues on the Magento2 repository overall is moving quite slow, there is a plenty of issues that go unanswered for months.
Even if it gets fixed, plenty of bugfixes that remain unreleased (not released? this shouldn't even be a thing in real world) also for months and many versions.
IMHO, your best shot is looking for some kind of a workaround.
I have same issue how to fix?
@GuidoHub, thank you for your report.
We were not able to reproduce this issue by following the steps you provided.
Please provide more information how did you create multiple websites that use the same store.
@GuidoHub we are closing this issue due to inactivity. If you'd like to update it, please reopen the issue.
Most helpful comment
Problem still occurs in version 2.1.5 Does nobody else have the same problem. Can't be I am the only one here. Which info do you need more to investigate?