Most likely the trouble is the common wire. First check all the wire connections then look at the possibility of the wire being cut at one of the fence posts.

1). Where is the Timer located?
2). Are three valves in same location,(connected side by side)?
3). Check if one cable with multiple wires in it, feeds those three valves that are not working.
4). If yes, than look at that valve location, and where the Timer is located, and see if that path crosses near the location of where the fence work performed.
* Then let me know what you find...