This error occurs for Sentinel-2 processing in ACOLITE 20160520.1 and is caused by the GUI allowing for conflicting settings: stitching the S2 granules without providing cropping limits. You can either disable the stitching option (Advanced Settings > Sentinel-2 tab) or provide limits to your region of interest.
This error will be fixed in later releases, where the stitch setting will be ignored if no region limits are provided.