How are you filling your bottles? Are you bottling carbonated beer?
If your beer is uncarbonated, you need to make sure that your hose or bottle filler goes all the way to the bottom of the bottle before opening the flow. That will prevent aeration and foam, as the tube end will be submerged during most of the fill.
If you are already using the above technique, you might be bottling a little early, before yeast-produced CO2 has had a chance to come out of solution, usually while fermentation is still somewhat active. Probably ill-advised, as this can create bottle bombs! Be patient. RDWHAHB, and bottle later.
I have no experience bottling carbonated beer, but if you're bottling from an already primed keg, you could try a "beer gun" device available from most of the online homebrewing supply shops.