I've run into this before too. From the matfile page there's a note
"Note: Version 7.3 MAT-files use an HDF5 based format that requires some overhead storage to describe the contents of the file. For cell arrays, structure arrays, or other containers that can store heterogeneous data types, Version 7.3 MAT-files are sometimes larger than Version 7 MAT-files."
Using the -v7 option was my remedy as well.