I mean, I had a few Draugr raids while I was taming my 1 star wolves, but the pen I made was strong enough to contain them. Have had little issue with other raids.

As for things spawning during a boss fight, sounds like you just needed to remove the workbenches you made to prepare. Can't have a raid if there's no base there to be raided. Does seem unlucky, but I've not faced these issues myself. Honestly, I haven't had a single thing broken by raids yet.

I think the worst thing I had happen was when a serpent broke my boat while I was fishing in the ocean and I got stranded on a turtle's back while my co-op friend had to fight off a Draugr raid solo. He'd not had food up so his HP was low and he got camped for awhile. I could just sit there and fish off the turtle and wait for rescue. I suppose the base took damage then and our 1 star boars all died, but we shortly replaced them with 2 star boars anyhow.

Does just seem like bad luck.