Correct me if I am wrong (please provide evidence that if I am wrong, provide a battle that the Separatists win during the Clone Wars era) but it seems to me that they never win any battles against the Republic.
It wasn't really.
The Confederacy of Independent Systems/Sepratists were know to have won the Battles of
They also successfully conducted attacks on Obi-Wan Kenobi's fleet and Mahranee, as well as the destruction of the Felucia medical station, the Bombing of Coruscant's central power distribution grid and the Devaron Massacre.
You should note that Star Wars: The Clone Wars frequently focused on the Republic's greatest heroes, such as Anakin Skywalker, Obi-Wan Kenobi, Mace Windu and the like. It isn't hard to assume that less talented Jedi were losing battles that we just didn't see.
Additionally, Palpatine was manipulating both sides of the war. It's likely he prevented the Separatists from being too successful, as that would make controlling the entire Galaxy later on more difficult.