An invalid mesh topology may be attributed to geometrical characteristics in the supermesh, which may inhibit the generation of a mesh consistent for the FEM.
Obviously, the line in your supermesh causes the problem. Indeed, problems can arise as a results of lines containing sharp kinks or lines which confluence at sharp angles.
Moreover, inconsistencies in geometrical topologies of the input shapefile may also cause the problem as Pete already indicated. Therefore, you may check the shapefile according to possible overlapping lines. You may also check if one large line is represented by several line segments (e.g. several line features). In that case, please assure the last vertex of one line spatially converges with the first vertex of the subsequent line. Small spatial deviations in the magnitude of several orders after the decimal operator between the last vertex of one line segment and the vertex of the subsequent line segment may trigger invalid topologies in the FE-mesh.
Apart from the input data, the mesh generators provided by FEFLOW have advantages and disadvantages with respect to robustness and capabilities of handling complex geometrical structures. Accordingly, it is worth to try another mesh generator.
Instead of using a line in the supermesh you could also split the polygon into two sub-polygons along the trace of the line enabling the application of the Advancing Front mesh generator which originally does not consider lines in the supermesh.
