Your wiring is probably wrong.
Wiring is tricky for 3-way timers.
First of all, both 3-way switches cannot be replaced with timers ... just one of the two switches is replaced.
You don't say which timer you have.
Since I know the wiring and the timers, let me jump in, and you can add a comment, and then we can work further.
A) You have battery-operated ST01C or EJ500.
Here is wiring diagram for Intermatic battery-operated timers:http://waterheatertimer.org/ST01C-program.html#3way
Note that at all times, the blue wire has to go to load, and that the blue wire connects to dark-colored screw on 3-way switch.
Note that the remaining 3-way switch is not wired the same as before. The red and blue wires have to be wired exactly as shown, and the wiring might require additional wire running between the switches.
Now add a comment with your wire colors and description where you are in the wiring.
B) You have Aube timer with rechargeable battery.
T0132 manual shows wiring diagramshttp://waterheatertimer.org/Aube-T1032-timer.pdf
Below is image of typical Aube wiring.
The manual shows one other diagram depending on which switch is being replaced.
The important this is note that the wiring on the remaining 3-way switch requires a jumper wire from the dark-colored screw to the brass screw on other side of switch. But it has to be the same brass screw that goes back to Aube timer #1 wire.
Usually this little difference solves the 3-way switching problem, but add a comment any time.