How do you define the Sky Train 'failing'?
The purpose of the Sky Train has been to put the team leader in a good position to finish off the climb with a good result. This usually means reeling in the breakaways as well as the attacks from the rivals.
In TA Stage 5, the Sky Train delivered Froome to the final climb but Froome cracked on the climb, that's not a failure of the Train. In Catalunya Stage 3, the Sky Train delivered Wiggins to the flamme rouge but Wiggins didn't have the legs to win the stage, that's not a failure of the Train.
Only real Train failure this season so far has been Catalunya Stage 4, which had its own weird circumstances as well.
The presence of the Sky Train doesn't make the Sky leader unbeatable, but it does reduce some of the options a rival will have to beat the Sky leader. It is probably not possible to make a long range attack and hope that the rivals behind look at each other for someone to lead the chase instead of organising a chase.
It is still possible to beat the leader by simply being a stronger climber, and attack when the leader is finally isolated. Of course, you have the situation where Porte and Froome are still pretty strong when isolated, and an isolated Wiggins may not lose enough time that can't be taken back in an ITT.