You are getting invasions. They will go after what ever they can. Boats included. They want to get to you and will attack anything they can. Your rafts have been either near their spawn point or there is a path inside the base that takes them into the water. As they will look to attack you and will will look for a path as close to you as possible.

This happens can happen every 46 minutes iirc and (a day is 18) so every 2.5 days. There is a RNG roll on the back end with a 40% chance of a Invasion happening. You have to be in your base for this to happen you need to be near three base structures, Bed Campfire Forge for example. (walls don't count)

So what is happening is the Boat is the only thing they can get to and it is near the only way (I assume) into your moat.

Unless you close that off as has been suggested with a gate then it will occur every time they attack. The trolls, draugr, skeletons etc... will all do the same thing.

Personally I build one of three ways. either a fully enclosed base with my boat a little ways away but not where I have seen spawns happening. That way they are looking to attack the base and there is no pathing for them.

I build a gated harbour inside my walls

Or I build a Harbour where the boat is in deep enough water the mobs can't get get a footing to attack. (which is what I've done several times previous effectively.)
https://steamcommunity.com/sharedfiles/filedetails/?id=2407366362