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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.

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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.