The Trouble with Sheep is a 1989 annual story.
A stray dog is chasing sheep in the valley and Thomas' driver warns Thomas to be careful. But Thomas is not worried and boasts that if he blows steam at the dog, it will run away. Thomas is soon puffing cheerfully on his branch line when he hears a dog barking. Then, lots of sheep run across the line followed by a black and white sheepdog! Thomas' driver applies the brakes and Thomas grinds to a halt just in time. The dog runs away, but the sheep, confused, just stay on the tracks. The fireman runs off to fetch a shepherd and two sheepdogs to take the sheep back, while the guard checks that nothing runs into the train. Once the sheep have all gone, Thomas tries to set off, but his brakes will not release. The guard goes to the signal box to tell the signalman. Meanwhile Thomas' driver finds that a brake pipe has come loose and reattaches it. Thomas starts off and goes all the way to Elsbridge, where they wait for a while. Thomas is impatient, but his driver reminds him to wait for the all clear from the guard. Then he realises - the guard is still at the signal box! When the guard finally arrives, Thomas apologises, but the guard says it was really the dog's fault.
- This story may have served as inspiration for the peep-through book Thomas and the Bad Dog.
- A reference to the story, Bulls Eyes is made.