It's not difficult to identify cheats, just more expensive.
The number of clocks is limited. The exact time and location the employee (or fake fingerprint) swipes in is known - because it's a time clock..
Stick a camera covering the clocks (some clocks have this built in). Ensure the video is timed.
Probably also worth changing the employee's unique id to something else when re-registering a different biometric source, so it's easy to spot the miscreant when they swipe in under the old id.