The formula for calculating the position of the whiskers is
Q3+1.5IQR and Q1-1.5IQR
But doesn't that mean that the length of the whiskers should be of the same length? How are they of different lengths in some boxplots?
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Not necessarily. The whiskers actually end at the highest point within $Q3+1.5R$ and at the lowest point above $Q1-1.5R$. So for instance if $Q3+1.5R=100$ and the highest value in your sample is $90$ then the whisker will end at $90$. You must be observing something like this.