I've a Canon printer and have always refilled my own cartridges.
A common problem is airlocks.
The foam inside the cartridge is mostly empty cells, when an area (sod's law decrees it to be usually at the bottom nearest the outlet) gets filled with air instead of ink it can stop that colour ink from printing. The Manufacturer gets around this by using a vacuum method to initially fill the cartridges.
Often it is assumed the print head is blocked.
At home, a simple way to overcome this problem is to utilise centrifugal force. Seal the cartridges outlet, put the cartridge in a poly bag and secure it to a suitable piece of cord. Now just whirl the cartridge around and around until the ink is forced to displace the air. DO IT OUTSIDE!!!
