I believe this was asked previously here:
Interface Builder degrades storyboards, resizes and repositions views in small increments
I have not yet seen a fix to the problem, but the answer I posted there likely holds true here.
https://stackoverflow.com/a/28577800/682574
At least one source is due to storyboards resolving layouts to either full pixel boundaries (x=7.0, y=10.0) or partial boundaries (x=7.5, y=10.5). As best I can tell, this can be recalculated any time you view the storyboard and the rounding is actually determined based on the current display environment.
You can intentionally cause this behavior by viewing the storyboard on a retina display and then viewing it on a non-retina display. With my dual-monitor display, if I just drag a storyboard from one screen (retina 5k) to another (non-retina) it will generate a flood of misaligned constraints. Unfortunately moving it back doesn't fix them! Try it out for yourself (or don't ... it's a pain to correct).
In a team environment its easy to see how this could happen as soon as two people with different setups view the same storyboard.
How to fix it? I haven't heard of a workflow that properly corrects or avoids the problem unfortunately.