You have a three-way miswired. Here's how to correct the problem:
1. Shut off the power and remove the wires from the switches. There will be three wires to each (not counting the ground if there is one.)
2. Turn the power back on, and one of the 6 wires will be hot. Mark that wire as 'common.' Turn the power back off.
3. Hook the 'common' wire to the common terminal of the switch. The terminal will either be marked 'common' or be a different color than the other two.
4. Hook the other two wires to the other two terminals. It doesn't matter which goes where.
5. Turn the power back on, and go the the other 3 wires. One will be hot. Move the switch at the other location, and another wire will be hot. Mark the wire that was never hot as 'common'.
6. Turn the power back off, and hook 3 wires to the second switch the same as steps 3 & 4.
7. Reinstall the switches into the boxes, put the covers back on, and restore the power. If you did it right, it will work right.