I am using the generate service areas tool in arcpy and I am getting these cutouts in the output polygons (examples below.) It appears that there are roads in some of the cutouts, but not others. What could be causing this? Is this just caused by disconnected road segments and is there a way to fix it?
Looks like your network dataset has portions which are disconnected from the rest of the network. Another reason could be the restriction attributes that prevent from travelling to those segments.
Check this post Solved: Strange gaps in detailed service area (network analyst)
In the above post, the user had some duplicate line segments that were causing the issue.
Most likely you are using the "High or Detailed Polygon" option when you are generating the service areas. This option will find all the unreachable areas and give you those small holes. If you do not need this level of detail, use the Standard option.