If you connect a camera directly to your computer and then use the Erase and Eject button to erase images after import, you may encounter situations in which not all the images are erased.
To avoid this issue, it's first and foremost recommended that you erase or format cards using the camera itself rather than Aperture, or your computer in general. In-camera deletion is superior, because some cameras use a more specialized format, while Aperture must use a generic format. Think of any computer-centric erasure method as a convenient backup method for card use that's not business critical, or when in-camera deletion is not possible.
Secondly, when deleting in camera, a format command is superior to an erase all (or similar) command. If you mix the use of your memory cards between different camera models, for example, the differing folder structures used by the cameras may result in situations in which an erase will not detect the file (thus leaving your card nearly full). However, a format will always erase the files in that scenario, and often a format is faster than an erase.
Third, a high-speed card reader (FireWire or USB 2.0) is generally a superior tool for importing images as compared to a direct camera connection. If you don't have a card reader and must import directly from camera, check your camera's settings to see if it allows you to specify the mode used by the camera when connecting to a computer. The two common modes are "peer to peer" (PTP) and "mass storage." Try setting your camera to the mass storage, or similarly named, mode.