Storyboards constraints suddenly all misplaced - ios

I am using XCode 6.4. I have quite a big Storyboard, and sometimes, when I open it, lots of warnings appear out of the blue, saying I have misplaced views, without touching anything. Everything was fine before, and the misplaced views are in every single viewcontroller. I add most of the constraints manually.
Any ideas what I might be doing wrong, or why suddenly everything moves?
EDIT
I pull from the repo, open XCode, and then all the warnings appear. If I git status, the storyboard has changed.
The difference between the versions is on the systemVersion attribute on the Storyboard. That change probably happens automatically when someone else with another configuration opens the project and then commits the changes.
This (long) question is related: Xcode changes unmodified storyboard and XIB files. However, my problem is not on the class attribute, but on the systemVersion

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In storyboard my views are messed up. Why is that?

I'm using Xcode 9 Version 9.1 (9B55). There is something strange happening in a storyboard. Some of my views are are messed up, and I don't know what is the reason.
It looks like this:
EDITED
However, all my constraints are set right, and when I run the project on different simulators and on a physical device, everything looks fine. Here how it looks on a simulator/physical device:
I don't know what is the reason for this kind of behaviour but it makes impossible to work in a storyboard. I think, this problem has appeared quite recently. Sometimes, after reloading the Xcode, views again look fine, but when I start working with storyboard (adding new views, changing constraints or even just tapping on a constraint to see its constant), they again become messed up. Does anybody have this kind of issue, and how this could be solved?
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