Hopefully you're aware of ATM skimmers. I'll discuss them below but thought I would start with a low tech way to lose money at an ATM. San Francisco police caught a crook who stuffed napkins into ATM cash dispenser slots. When people tried to withdraw cash, it would get stuck behind the napkins. After they walked away frustrated, the crook dislodged the napkins, and walked away with their cash.
If your ATM money does not come out reach up into the slot and see if there's anything stuck there. If that fails, take a cellphone picture of the ATM screen for evidence and then call the number on the ATM for service or go inside the bank for help.
Now back to skimmers. These are devices designed to steal your card information and pin. Check out the photos at http://www.snopes.com/fraud/atm/atmcamera.asp and http://consumerist.com/2009/04/heres-what-a-card-skimmer-looks-like-on-an-atm.html
There are two things to worry about.
1. A camera that records the PIN you type in. At the snopes link above the camera is hidden inside a pamphlet holder next to the ATM (pictured above). At the consumerist site the camera is in a strip attached to the ceiling.
2. A card scanner attached to the ATM. At both sites the extra scanner is part of a panel affixed to the ATM and look absolutely authentic! At this site, http://gizmodo.com/5453857/atm-card-skimmers-are-getting-frighteningly-sophisticated, the skimmer is quite thin and covers the card reader.
What can you do to protect yourself. Not much I'm afraid. Try to cover your fingers as you type the PIN from prying eyes or camera. Use the same ATM and remember what it looks like. If anything changes on the outside of the machine, ask the bank before using the machine.
Any card scanner could be stealing information - at restaurants, gas pumps, grocery stores, etc. If money is stolen report it to the bank and file a police report.