After a modelbuilder run, using GIS-ID as the label, when you open and look at the manhole flextable you have twice as many junctions as there should be. That is, junctions were created directly on top of each other.
This could be the result of a data mismatch with your GIS-IDs. If the field your GIS-ID is set to uses a different unique identifier than what your upstream and downstream node fields are set to in your pipe field mapping then modelbuilder will create duplicate junctions because it doesn't recognize the upstream and downstream node IDs you have provided it.
More simply in specifying the GIS-ID field you are telling it to use one unique identifier for the junction label (ex. 1234, 1235, 1236, etc..) but, your upstream and downstream node ID fields on your pipe mapping are using another field name that uses a different unique identifier than your GIS ID(ex. MH-1, MH-2, etc...).
To resolve this issue, make sure that you GIS-ID field and your upstream and downstream node fields for you pipe reference the same unique identifiers.
Building a Model with ModelBuilder
Junctions appear to overlay a pipe instead of connecting to it
Unexpected pipe connectivity after ModelBuilder import