You have driftwood in your tank? It will be causing the dark stain in your water, konwn as tannins. You can think of the driftwood as leeching out "sap" that colours the water. It's natural.
Is your tank planted? Dirt is normal in a filter. Just change the sponge regularly. If you mean that the sponge gets clogged up too quickly, then yes, you're probably feeding your fish too much/too many fish that contributes to the high wasteload.
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