Gun control advocates were especially concerned about the appearance of lower receivers for semi-automatic weapons that have appeared on Thingiverse. The lower receiver is the the “body” of a gun, and its most regulated component. So 3D-printing that piece at home and attaching other parts ordered by mail might allow a lethal weapon to be obtained without any legal barriers or identification.
Makerbot’s move to delete those files may have been inspired in part by a group calling itself Defense Distributed, which announced its intention to create an entirely 3D-printable gun in August and planned to potentially upload it to Thingiverse. Defense Distributed says it's not deterred by Makerbot's move and will host the plans on its own site.