I am using ArcGIS 10.5 Clip tool to locate flooding on the road with a polygon file for the flooding (Clip Features) and a polyline file for the road network (Input Features). The polygon file consists of many triangularly shaped ponds. To filter it a bit, I have selected only the polygons, intersecting the road and have copied them to a new layer file. When I run the Clip tool, most of the flooded roads sections are extracted correctly, but others are not clipped at all as if some of the polygons are disregarded. See the image for more information.
The blue polygons are ponds of water on the road and the green lines are the result of the Clip tool. The road network is not interrupted.
I observed it visually and could not draw any conclusions why it might be happening and how to fix that. Performed the same thing with Intersect and it selected whole roads instead of the flooded segments of the road.