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That happened to me twice-
1st time - one of the doors wouldn't open so had to hold my bike all the way back from Bristol as they refused to let the train leave with my bike in a wheel chair spot, even after saying "I'll move it any one needs the spot (because I'm not a total cunt)"
2nd time - with my MTB, tyre wouldn't fit and the bars were too wide, ended up putting a cable tie round the rim and tyre and putting that in the hook.
When Virgin were running the LNER they just had like Sheffield stands in the hood for your bike. In the new trains they've got two of those stupid cupboard with the corner doors, when I arrived with my mountain bike the tyre wouldn't fit in the hook, even with all the air let out, and the handlebars were too wide, and they're supposed to fit two bikes. In the end I just hung it with a cable tie on the wheel, and a cable tie on the brake lever to stop it from moving round.