Layout breaks in Emacs 25.1

[kini]

Layout breaks in Emacs 25.1

[MRFaria]

I think this happens because by default emacs25 changed the shell buffers to open in a new window instead of the same one.

Not sure how to fix shell-pop, but you can get the correct behavior with:
(push (cons "\\*shell\\*" display-buffer--same-window-action) display-buffer-alist)

Which makes the shell buffer open in the same window, which is what shell-pop expects

[articuluxe]

If anyone happens to use shackle, the following is an equivalent rule:
(add-to-list 'shackle-rules '("\\*shell\\*" :regexp t :same t))

[rafipanoyan]

I have the same issue with Emacs 25.1.1