When building a watchtower, there is for some reason an invisible obstruction in the center of the floor. You cannot run through it, but you can crawl under it, essentially rendering the watchtower floor to being restricted to two halves. Removing an upper half of the watchtower wall resolved the issue for me, however I have not tested rebuilding the wall. This has occurred with two watchtowers for me personally so far, and can provide a clip if necessary.