Passengers on that train were stranded, the trains following from Leeds had to stop then were unable to re-start which in turn led to later trains also being cancelled or delays.
It affected trains between Leeds and Ilkley and Bradford Forster Square and Ilkley.
It has prompted a further flurry of anger for rail users who have pre-paid tickets and passes yet are unable to use them or complete journeys.
The service was affected at the height of the rush hour and despite Northern Rail saying the situation had been rectified by around 7pm, some passengers were still making their way home beyond that.
Taking to twitter, Sarah Walker said: "Leeds to Skipton. Not only did there end up being two trainloads of passengers expected to get on a two carriage train, when they did finally get on a train (led by a guard) on a different platform, they were all then told to get off and go back to the platform they just came from."
John McGlashan added: "I set off at 17:03 and got home at 20:10. That’s not inconvenience that’s shocking service."
A spokesperson for Northern said: "There was a train at Guiseley where the brakes could not release. This caused delays for later services who was waiting behind this on the hill causing services not being able to start on the hill."
It comes as tomorrow's services will be affected by continuous weekend strike action by Northern Rail.