Expect every daily retrieval of AOD to have many missing pixels, mostly where clouds appear. Data is removed when the quality assurance flags do not meet some minimum criteria. This can happen when the retrieval is contaminated (e.g. from clouds or sun glint on the surface). If you are interested, you can obtain raw level-1 and level-2 data with all data, including arrays for quality assurance flags.
There will also be systematic gaps in the data where the satellite had no coverage. Polar orbiting satellites will get complete coverage near the poles, but widening gaps will appear the closer you get to the equator.