As of MATLAB R2016a, MATLAB Compiler will now check out licenses for toolboxes used in the code you compile. This means that if you compile code in MATLAB using MATLAB Compiler, any functions which require a license for a particular toolbox to run will cause the required toolbox to be checked out at compile-time.
Please note that this applies to compilation performed using the standalone mcc command from the system command prompt as well. Calling mcc from the system command prompt reserves the MATLAB Compiler license for 30 minutes after it is called, and as of R2016a it also reserves any relevant toolbox seats for the same duration. Calling mcc from within the MATLAB environment does not cause any license seats to linger, either for MATLAB Compiler itself or toolboxes required for compilation.
In MATLAB releases R2015b and earlier, toolbox checkouts are not performed when compiling code which requires a license for one or more toolboxes.