Not sure about the exact conditions of the bug, but it usually shows up when bots build stuff that instantly get attacked. Which usually kills the bto.

Entities do not depend on the bot still being alive to be turned on.

There was a case where cloned entities would not be turned on ever so I did push an update to fix that.

I would like to see the entity being placed at the end of the "build process" not immediately place a empty structure first then change it to the actual structure.

I would like to make the build process more animated but that's a bit more involved than I'd like. You're welcome to write the code and submit it, or even publish your own fork of the mod.