It does, however, complicate ending the story.
One option: you have to reduce it to two during the course of the story. Some factions have to subsume others, by allying with them, or destroying them (rare, because it weakens the side), or otherwise getting some of them out of the way. Do it early enough, and you lose all the advantages of having them, and the conflicts grows weaker. Near the climax, and they will start to drain the energy off of it.
Or, you have to, in a masterpiece of orchestration, get them all in the same place at the same time, in pursuit of their individual desires in such a way that all the major issues are resolved when it is done.
Of course, if you have enough factions, you can pare them down a little by the first option before throwing in the second to mop up the remainders.