A few quetions on metta I was practicing metta meditation today and the thought came up: "What if your wish for happiness for one person (Person A) causes another to suffer indirectly (person B)?" 

My understanding of the problem: the wish of metta is conditional, that is, it is for person A. Since metta is meant to be an unconditional love, how can we wish metta for individuals? Doesn't metta only make sense if it is wished for all beings?

How can we wish metta and have that wish be moral without understanding the consequences of what that wish may cause. Is metta not meant to be a literal wish? I have a feeling that I am not fully understanding metta properly, so I'd like to hear where I am falling short in my understanding. 

Kind wishes.
As I understand things: Metta-meditation is not "magic", not something like "positive voodoo". In the first instance it is a training for you and your ability for loving kindness.
Based on this it is also a stepwise training: you start with simple ones (loving kindness with yourself, your mama, your spouse, your best friend). After you have some fluent experience you change the subject to more neutral persons, and then even to some people you dislike (or you think they dislike you), or to rivals.
The effect of the training - if successful for you : then your new way of impulses might have effects to the world...