Here are the known problems as of October 28, 2009
Support for Webcams in Scratch on Linux is still new, so if you have problems see the Linux_Camera_Plug-in wiki page for help.

• Midi playback is "faked" (doesn't use real midi libraries)
  
• There is no support for the Lego WeDo kit
• When system is using Compiz, Scratch does not repaint window after leaving fullscreen / presentation mode. Some users report that this problem is fixed in the next version of Ubuntu (9.10)
  
• Help related functions in the Help menu do not work.
• Users report sound recording is "choppy" in Karmic Koala, Ubuntu 9.10