随着Xcode 7.2的发布，可以通过打开每个场景文件来解决问题（ .sks ）并保存一次。放大和缩小时，黄色框和内容（请参阅我的问题中的屏幕截图）再次与另一个很好地对齐。

With the release of Xcode 7.2 the issue can be fixed by opening each scene file (.sks) and saving it once. The yellow frame and the content (see the screenshots in my question) are again aligned nicely to another when zooming in and out.