This sounds to me like a sizing issue rather than a filling issue. Blender displays things on the workbench like wires and faces but uses normals to calculate what parts of the model are considered the inside. If you don't know if your normals are correct you can select the whole model in edit mode with A and then use Shift+N to fix the issue. If the problem isn't normals then you might be running into a printer limitation.
3D printers are all limited in the size they can print for FDM printing the limiting factor is nozzle size, for SLI printers its the focus of the laser, etc. Let's look at the case of FDM with a 0.4mm nozzle because that is the most common type of 3d printer. A 0.4mm nozzle is not able to extrude plastic in lines smaller than 0.4mm in width. But the nozzle limits more than just the minimum diameter, it also limits the maximum layer thickness to 0.32mm and the maximum width of the extruded filament to ~0.6mm. Of course, you can try and push the max stuff but you will suffer quality issues
here are the general equations I like to use while planning a print.
min extrusion width = nozzle diameter
max layer height = nozzle diameter X 0.8
max extrusion width = nozzle diameter X 1.5
If the slicing program you are using knows that the printer has this limitation and it detects a part of your model that requires a wall that is smaller than the limit it will raise a warning flag. If you ignore the flag it will usually just skip the area that is too thin to print leaving your model incomplete. The only real fix for this is to scale up the print so that the thin walls are big enough to print, adjust your model, or get a smaller nozzle for your printer.