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Firstly, MuPDF is released under the GNU AGPL; with this you are free to copy the code, modify it, and incorporate it into your own works as you see fit. While these works are purely for you alone there are no limits on what you can do, but once you share your modifications with anyone else (either in source or binary forms, or by making them available as part of a `service'), this counts as distribution. In order to distribute anything derived from MuPDF you must obey the terms of the GNU AGPL.
The `viral' nature of the GNU AGPL is such that this means your entire application that uses MuPDF must be distributed under the GNU AGPL, not just the portion that interfaces with MuPDF. One of the most obvious consequences of this is that you have to make all the source code for your application and all the libraries that it relies on available. For many developers, they simply cannot agree to this, which rules out the GNU AGPL for them.