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There may be different reasons but I believe the most common is the clogged pump filter, AKA sump pump screen. It can be clogged with food debris or calcium deposits from hard water. It's on the bottom of the washer, and can usually be easily removed for cleaning and/or soaked in vinegar to remove the hard water deposits.
Lane, If the small amount of water in the bottom is about a half an inch or so and clean looking it may be normal. Some dishwashers do this to act as a sort of seal. If the water looks cloudy or dirty then you may have a filter problem. In this case you should be noticing cloudy film on your clear glasses from them being rinsed in dirty water. Easiest way to figure this out is to either call the manufacturer and ask if this is normal or read to manual that came with to dishwasher in the troubleshooting section as some one has probably asked this before.