If you have a problem as for example after saving the scene , it looks like it did not save then look for the component "Content Size Fitter" into your game objects and disable it. This can fix the problem.
bug report with simple example: https://fogbugz.unity3d.com/default.asp?830303_arfitgekmmo7oekc
UI "Content Size Fitter" asking to save the scene after finish playing.
Unity 5.3.6 and U 5.4.0 in Windows
bug report with simple example: https://fogbugz.unity3d.com/default.asp?830303_arfitgekmmo7oekc
UI "Content Size Fitter" asking to save the scene after finish playing.
Unity 5.3.6 and U 5.4.0 in Windows