That’s a good question. While each term is commonly substituted for the other there is a difference. WordPress is made up of a series of PHP files that query the database and display that info each time a visitor comes to your site. A theme, in addition to the PHP files, also uses CSS and images to organize that data and present it in such a way that it is organized, readable and just pleasing to the eyes. A particular theme can have several layouts if it is designed as such an example being iTheme’s new FlexxTheme. This theme has over 1,000 possible layout combinations such as pages and or categories being display above or below the header, one or two sidebars, sidebars displayed on the left or right side of page etc
So while it is one theme it has numerous layout options.