Two Pokemon with same CP, one is wonder one is not, does it matter which I use in a battle?

Since you didn't post images, it's not possible to know for sure, but if you have two of the same species of Pokémon with the same CP but one is a wonder and the other is not likely to make much headway in battle, then they are likely not the same level.

The wonder Pokémon should have less of the semicircle above it filled in compared to the one that's not likely to make much headway in battle. Thus, you should absolutely train up the one that's a wonder.

While they may have the same CP now, they will have a large gap in their CP cap when they are the same level.

Also, it's worth noting that movesets will not influence whether a Pokémon is a wonder or not.

When you select the option to examine a pokemon, the head of your team will look at the so-called IV (individual values) of the pokemon. In the end, the individual values do not make a huge difference when it comes to the combat strength of a pokemon.

If you have two pokemon of the same type, using the pokemon with the highest CP is usually the best option, as it takes less stardust to upgrade it. If you have two pokemons of the same type with the same CP, use the one with the best IV's.

Short answer is that it will not matter.

Prestige and xp is dependant on attacker CP compared to defender CP.

Because of how stats are distributed, you might have a minimal diffrence in how the fight goes if you can dodge because HP and Defence stats won't matter as much as if you take all hits.

(so if one has IVs of 15/0/0 and the other 10/15/15, the first might end up a better fighter for you.)