There are plenty of bench or dining table spots available in the kitchen.....
I would rather they don't put coffee cups in the kitchen. My sims have a hard enough time finding a free kitchen counter or table as it is, without adding coffee cups to the rest of the clutter.
You could put the coffee machine in the living room or dining room instead. If all your coffee-able surfaces are either occupied or or close to the coffee machine the sims won't walk miles to put the cup down.