Unable to reproduce in the latest software.
There are a few possible issue points having to do with the data however.
1. Spatial Reference properties are not set to their default. XYTolerance is too large. Can affect processing and lead to unexpected results.
2. The provided output has a number of the input Roads shifted drastically. This indicates a very large XYTolerance may have been used during processing (which would then cause the roads that actually overlap the poly boundaries to no longer overlap)... such as through specifying a large XYTolerance parameter in the tool.
I highly recommend:
1. Never process data with Spatial Reference properties not set to their default.
2. Never use the XY Tolerance parameter when available in a tool.
3. Never use the XYTolerance to generalize data.
For more info:
http://desktop.arcgis.com/en/arcmap/10.3/manage-data/geodatabases/feature-class-basics.htm
https://support.esri.com/en/white-paper/1301