I'm using QGIS 2.18.12 and have this problem:
When I copy objects and paste them into a new layer, I get the message CRS undefined. (I'm using EPSG:28992, Amersfoort/RD New as CRS). In the long term release 2.14 version, I get the same message, but I get a window to change the CRS. In the 2.18.12 version, there is no window to change the CRS, actually, and this is pretty annoying, QGIS stops the whole action. In short, I can't paste objects anymore into new layers.