MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Hey, sorry to read that.
There's a huge number of reasons why this could be happening, ranging from printer's precision to enviromental conditions, I'm afraid that I'm not going to be able to give you a concise answer.
Are you printing this in PLA? I do not recommend to do so. 9 chances on the 10 that a properly sized PLA case will break too easily because this thing needs more flexibility than PLA is able to deliver.
In order to get a right fit you may like to use the test STL files and follow the instructions.