Well obviously if you just toss fire and water magic together they will interfere with each other. That's why proper technique is to isolate spell components with an appropriate null magic field while they are forming. The targeting system of course keeps track of each component, and makes sure there is a slight time or distance difference between them. If you get hit with a fireball in the chest/head and a water blast in the stomach/leggs, they are not going to cancel each other out.
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There could be a warning when creating a similar spell to one you have, but you may want some similar spells. You would not want to teach both characters Identify or Repair, but you may want to have your mage learn 2 missle fire spells (one with more damage, the other with lower mana requirements), or duplicate a fire spell planning to add earth damage your next level.
I could see it getting a little messy for the game to try determining if a duplicate skill type was learned accidentally or on purpose.
