So I have encountered this bug before but this time I thought I would write up a thread about it. about an hour before I logged off this morning I re-arranged my base moving the ship factory from the pictured location to where the arrow starts in the top right ad replacing it with two storage buildings. I came and went from my base several times after the building movement and then logged off. when I returned just now I noticed that the ship factory was sitting on top of the 2 storage buildings. Hope this helps.