3D printing software requires a few constraints that STL files must adhere to in order to be able to be processed for printing. If any of the constraints are broken, the file will either fail to slice or it will slice incorrectly and some or all of the part will not print.
Luckily, there are programs that can repair errors in STL files. The most common programs are Meshlab and Netfabb Basic. Either of these can be used to repair many problems with STL files. Instructions can be found here: http://www.shapeways.com/tutorials/how_to_use_meshlab_and_netfabb or here: http://3daddfab.com/blog/index.php?/archives/10-Automatically-Repair-STL-Files-in-2-Minutes-with-netfabb.html
Meshmixer, available from Autodesk, is another Desktop application that will display STL errors and automatically fix them. Instructions for fixing STL files with Meshmixer:
1.) Import STL file
2.) Click Analysis->Inspector
3.) Click Autorepair All
4.) Export STL file again.