If you would unhide all geometry with Alt+H (and maybe enable the Face Orientation overlay), you would see that these non manifold vertices are connect to an edge loop of vertices which has a flipped face lying unconnected over the other face and the rest is just edges without faces. I guess this was supposed to become or is a remain of a window pane?

By the way, since you are using the Statistics overlay, an indicator for hidden geometry is the fact that when you select all with A, it shows only 696 vertices of 700 selected. There are 4 not visible and therefore not selectable.

If you would unhide all geometry with Alt+H (and maybe enable the Face Orientation overlay), you would see that these non manifold vertices are connect to an edge loop of vertices which has a flipped face lying unconnected over the other face and the rest is just edges without faces. I guess this was supposed to become or is a remain of a window pane? What makes these 3 vertices you showed now non manifold is the fact that they are connected to the other hidden non manifold edges.

By the way, since you are using the Statistics overlay, an indicator for hidden geometry is the fact that when you select all with A, it shows only 696 vertices of 700 selected. There are 4 not visible and therefore not selectable.