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Before the final test during the training of Bruce, Ra's Al Ghul gives him a bowl containing blue flower and some other things to smell in.

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After that, Bruce faces his fears such as bats and death of his parents. But here he is able to control himself and fight.

However, when Dr. Crane releases the toxin, Bruce wasn't able to control his fear and got knocked out for two days.

Later, Ra's Al Ghul reveals that the toxin was made out of that blue flower and it appeared that Bruce had the same effect both times.

So, why Bruce was able to control his fear during training, but not when Dr. Crane attacks? Is there something more in the toxin?

  • Possibly because he was taken by surprise, unlike the training. – NVZ Aug 12 '17 at 13:50
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I don't think this is ever explained in the movie directly but I would suggest this is a matter of concentration

Not Bruce's concentration but rather the concentrated liquid which makes the Fear Gas/Toxin.

Bruce actually says..

I’ve felt those effects before...but this was much more potent

and

It’s some kind of weaponized hallucinogen. Administered in aerosol form.

Yes, we know that the blue flower is involved in the process of making the Toxin but it's probably not the only element. The toxin is a concentrated form of the flower and, probably, other chemicals.

The equivalent would be burning an opium poppy to taking heroin. You might be affected by burning the poppy but you're sure gonna feel something when taking heroin.

There's a wikia which suggest there are additional compounds in the gas/toxin

The gas is actually made from the Blue Poppies near Ra's al Ghul's dojo. Dr. Jonathan Crane is the corrupt chief therapist at Arkham Asylum, he has a vast amount of knowledge in science due to working with medicine for his patients. Crane makes an alliance with Ra's al Ghul and Falcone and uses the flowers to make his deadly fear toxin. Crane also has Falcone sneak in necessary ingredients for the toxin.

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