Please see the word order carefully.
* 50 = "[a / the] 50% cancellation fee" or "cancellation fee of 50%" (i.e., 50% of the full fee you'd be charged if you didn't cancel)
* 50% = "50% of the cancellation fee" (i.e., half of the fixed cancellation fee; indeed, this doesn't make much sense in practice)
The former (which is what the sentence uses) means, for example, that if you booked a hotel for 10,000 yen and cancelled it the day before, you'd have to pay 5,000 yen as the cancellation fee.
See also: What's the difference between and ?