I've run into this problem on several occasions. I sometimes run into this when setting up large assemblies for flow modeling.
Navigate to the Flow Simulation tab, and click the icon called "Check Geometry." This is also located under Flow Simulation > Tools > Check Geometry. In the dialog that appears, click "Fluid Volume" and you can view the fluid volume of your model. A list of Invalid Contacts is shown in the dialog. Try toggling "Exclude cavities without flow conditions" to see if this provides further insight, which will depend on your model. You can Disable components systematically to troubleshoot your problem. (Disable is similar to Suppress, but a little faster.)
Usually for me, the problem is that I have some invalid line contact somewhere, so I just modify the model a little to satisfy the flow solver. Or sometime there's a bolt missing, leaving an open hole somewhere, which messes up the fluid volume.
I've had mixed results with Automatic Lids. You could also try making Automatic Lids at the part level, as opposed to the assembly level. But I think it's faster to create a part configuration with the holes suppressed.
Hope this helps!