NPCs have a tendency to fall into the watter while boarding rafts. Ensure you take the time to aid them in. They tend to follow you in a straight line when you use that command, so do it frequently (especially when riding the raft, as they may react to something on the mainland and try to assist) to ensure that they do not fall off the raft.
For strategy sake, it's best to bring one of each class with you: especially a cleric. When rushing a flank by using the raft system you'll need one cleric to build, another to heal, a warrior to fend off foes, and a mage to supply support and neutralize any ballistas. This four man group can vary depending on your tastes, but if you don't bring a cleric you'll have to knock on the front door to get in, resulting in the enemy being alerted to your diabolical deeds.