Krita always crashes when flattening an image. Either by shortcut (Shift+Cmd+E) or by selecting Layer > Flatten Image from the menu.
Same here using krita-3.0.1.90-x86_64.appimage
Git commit 8564a291348180f716d8f1270b303eea40e421c0 by Boudewijn Rempt. Committed on 09/10/2016 at 10:50. Pushed by rempt into branch 'master'. Check whether there's an active node before dereferencing Bug introduced when merging the latest animation code. Related: bug 370283 M +28 -26 plugins/dockers/defaultdockers/kis_layer_box.cpp http://commits.kde.org/krita/8564a291348180f716d8f1270b303eea40e421c0
Thank you, Boud! :D