To get more into detail: This shows that your map has at least 1 leak (isn't completely sealed.) Aside from breaking VIS, which will make your map perform badly (because it will always render everything in front of you, no matter if you actually see it or not,) this will also cause the water bugs displayed in your screenshots.
To find a leak click in your map, after you compiled it, inside hammer click on Map -> Load Pointfile. This will add a red line to your map which you can both see in 2d and 3d views. The line starts at any entity inside your map (can be a model, a trigger, a light, anything) and leaves the map into the void at some point. That's where your leak is. Seal that leak, then compile again.
Please note that your map might have more than one leak in it. To find them, you have to compile your map once for each (or rather, have VBSP run once for each) and then load the pointfile again.
I'd suggest that you compile on "Fast" until you no longer get leak warnings, then compile on normal to check the results.