I know of a Facepunch bug that may cause this and has been around for a long time but depending on how you place the triangles will determine if you have issues down the track as you were in your report.
The easiest way I can replicate this is by making a ring using square and triangle foundations and then fill it in, most times I get down to insert the last foundations and it will give me the same error. I believe triangles want to snap to 2 different points in some scenarios which in my opinion tricks it into seeing 2 buildings.