I have had this with mine as well and usually it is one of two things,
1) remove the quick disconnect from the lid and check the intake port on the filter, if there is something caught up in there like some leaves or dead fish it will cause a vortex or swirling motion as the water enters the filter producing noise and air bubbles. Sounds corny but its happened to me, once I removed the debris from the intake port everything was good.
2) you may have an air pocket at the top of the filter. When I fill my canister up I release one of the clamps till the water just starts to come out the top, then I quickly lock it back up, that way you are 100% sure the canister is totally full of water.
Another thing to check is the cap that screws on the top of the intake tube, if it is not completely tight it will suck air and cause alot of noise and bubbles.