Yesterday, I had 1700 reputation on Stack Overflow, but today I only have 1289. Why did this happen?
There are several options not all of them are visible:
Bounty If you assign a bounty to a question you lose the rep immediately. This should be visible in your profile.
Offensive or Spam flags If a question or answer received enough flags, it is deleted and you have a -100 rep penalty. Not sure if this is still visible.
Reputation recalc Not all changes in rep are shown immediately (for example upvotes to deleted questions and answers). They are shown if your rep is recalculated. If you want to know your current reputation and the source. Have a look at http://stackoverflow.com/reputation
Possible vote fraud If there has been some suspicious votes, they will be deleted automatically (for example a single account that dedicates most of the upvotes to your account. This does not mean that you have committed fraud.
A bug Maybe you just found a bug.
And remember you can always contact the SO team if you think the rep loss is suspicious.
Take a look at your reputation page and you should be able to see why your rep went down.