When importing a shapefile (SHP) containing multipart features (exported from ArcMap) the elements are incomplete (not all of the elements are imported). The following message may also be returned in the ModelBuilder Summary dialog:
"Warning: The source geometry for element "____" has multiple parts, but the parts are disconnected. The first continuous part was imported, but the source data should be verified."
ModelBuilder will import singlepart polyline/polygon shapefiles without issue, however importing Multipart polyline/polygon shapefiles will result in the above behavior.
In such cases as multiple shapes (polygons, polylines or points) are grouped together with one ID, so only one will be imported through Modelbuilder.
To import all parts of a multi-part shape, the shapefiles need to be converted into single-part before exporting to a shapefile. This can be done with GIS tools such as ESRI ArcGIS's ArcToolbox tool called "Multipart to SinglePart", as seen below. Convert the multi-part features into single-part using this tool, then import the converted singlepart shapefile.
Multipart To Singlepart
Building and updating a model using ModelBuilder
Preparing GIS data for use in the hydraulics and hydrology products