They have filed some controversial/anti-innovative patents.
Their printers phone home with encrypted information. Last I checked, there were speculated security and privacy issues with it, though someone should correct me if this was resolved.
They only open source their slicer because of the GPL licence, but they don't open source anything else (firmware, hardware, etc).
Again, I just recommend people look into these things before they buy a printer. Do your own research and come to your own conclusions :)