Does you part have lots of overlapping pieces? MatterControl is trying to merge them on export so that it will produce a good STL that can be used in other software.
You may want to check if there are a lot of loose parts that are duplicates of each other. Or you might be able to combine some of the parts together before exporting.
We will work on having a solution that can export without merging when there are too many parts or the bed is too complex.
Sorry for the inconvenience.