Choosing a second option choice I am currently applying to MSc pure maths/maths courses. 
One the universities gave me the option to fill out a second choice program. My first choice was pure maths but I put my second choice as applied maths. 
I was wondering, could putting applied maths as my second choice hurt my application because they might think I am not committed enough or 100% sure of doing pure maths?

The university says on the application form that if you are unsuccessful they give you the opportunity to submit a new personal statement for the second choice.  

I am considering ringing up the university and telling them to remove my second choice. 

What shall I do, does it matter?
Admissions committees have been in the business of matching grad students with classes and advisors for a long time. To provide the best fit, they have asked students for their specialization preference knowing that while some students are sure of their path (pure, applied, or statistics), others will change their mind with a broader exposure. Listing a second option should increase your chances of acceptance, for it gives the admissions committee more options.

While I cannot imagine an admissions committee penalizing students listing a secondary option, they will likely be displeased with wishy-washy students calling to change minor application details.