V3.13 CMS
You go into layouts and check it as a draft, go to design… do some list changes(maybe 30 list you have), when you save: This Layout is not a Draft, please checkout.
You want to kill someone after you repeat 5-10 times and the same error.
I have tried Checkout from the row menu and then design and clicked Design then Checkout from the banner at the top of the Layout and have had no issue making and saving edits either way.
I am using the recent release v3.1.4 so I would suggest upgrading and trying that in the first instance.