It is normal to have a few small air bubbles inside the cartridge after filling (you can't completely fill every area of the cart). A R3000 refill cart can hold about 30ml of ink. As long as the exit chamber is at least 1/2 filled, and the body is mostly filled with a small air pocket at the top, then you should be fine. To vacuum fill a refill cart, the air vent hole much be plugged closed. The air vet hole must be OPEN before installing carts into your printer, for proper ink flow.
I hope this helps. Best regards and happy printing~ Dana