That seems odd, from my experience I found it should affect the amount of experience gained when it's killed. Of course this is dependent on the gameplay constants as well.
Level is shown under creep's name, usually to indicate the strength of that creep. Level also effects the creep AI, if the level is higher than 5 they are going to be smarter (i.e run away from battle when low hp).
If the level is over 6 or 7 they also have Hero-Like Spell Resistance. If the level is over 5 then they have smart target choice, picking targets with lower HP who are likely to die faster.
And level does affect the EXP you get from killing it.
