I am having this issue too! Please help me. (I just purchased the game on GOG last week btw)
So you're certain you've looked where each wrench is supposed to be: one on the pipes, one in the book, and one in the drain?
If you have and still find that one is missing, you could always download the .sol (save) file for that location (#13) from this thread: http://machinarium.net/forum/index.php/topic,1274.msg6092.html#msg6092
...and then replace it with your existing .sol file.
Instructions for finding the .sol file on a PC using Windows are here:http://amanita-design.net/forum/index.php/topic,1097.0.html
Instructions for finding the .sol file on a Mac computer are here:http://machinarium.net/forum/index.php/topic,1095.msg5337.html#msg5337
Do that and load that first save slot...you'll start off in the sewer, and hopefully all wrenches will be present.