I have added some missing features I was made aware of by some commenters. The added features are:

• You will no longer click a bomb on your first turn.
• The game timer has been corrected to mimic the original minesweeper games. (start on 1 instead of 0)
• Question marks have been added. They are off by default and can be toggled on in the game menu.
• The custom theme template has been updated to include the two new sprites needed for the question marks.
• When you have placed the correct amount of flags around a numbered tile you can click with both mouse buttons to reveal all of the tile's non flagged neighbours. This currently only works with the downloadable version as a bug in GameMaker stops this feature from working in the HTML5 version. A bug report has been submitted to YoYo Games.

If you encounter any bugs or have any feature requests let me know in the comments. Thanks for playing!