Netlist comparison can find errors in your manufacturing data, that your PCB Layout tools may miss. It is an extremely important step used to validate your PCB manufacturing data before sending to fabrication.
The most common reason when you're receiving inaccurate results while performing Netlist comparison is --- Drill file setup.
Net Comparison Issue #1: Drill File Scale
Please remember the Drill NC format itself is extremely old (from late 70's early 80's). If you open one up in a text editor (like notepad) you'll see It's essentially just X and Y coordinates without decimal places. Many Drill files do not even include the units in the header. If you're aware of the drill format beforehand you may enter the values into the Drill Import settings. However if you're not sure, it's up to the CAM tool to guess the units and scale (i.e decimal place). FAB 3000 will typically guess the Drill formats correctly, however when it's wrong it's usually off by a scale of 10X.
Note: If you have already imported the drills and they take up a large area, you may use the command "Scale Layers..." (menu: Edit | Layers | Scale Layers X/Y...), and assigned "0.1" scale in X and Y for all drill layers.
Net Comparison Issue #2: Drill Layer Type Definition (specifically Non-Plated and Blind/Buried)
The default layer type assigned to each drill file after import is "Plated Thru-Hole". If you have a Drill file that is Non-Plated or Blind Buried than you must assign those layer types, so FAB 3000 know exactly how to connect the objects that come in contact with those drill files. Here's a tutorial showing how to setup Blind/Buried Drills, https://support.numericalinnovations.com/support/discussions/topics/14000002569
Net Comparison Issue #3: IPC Netlist File Misalignment.
The For whatever reason many PCB CAD tools will export their IPC Netlist files with a different origin than the manufacturing files (such as ODB++, Gerber, Drill, etc.). If the IPC Netlist file is misaligned than the Net Comparison will give inaccurate results. Here's a quick tutorial showing how to align the IPC Netlist file back with the rest of the design.
Note: Issue #1 and #2 can be resolved by using ODB++ or IPC-2581 files. If you're PCB CAD tool can export either of these formats I would suggest you use that instead of Gerbers/Drills (to avoid all the layer setup, etc.)