"We stop at the port."
Translation:Wij stoppen bij de haven.
That would mean something like "we stop on top of the port/harbour."
Mmmm... I'm not sure (since I'm just a learner) but I think that would imply that you stopped inside, within the harbour.
Prepositions are (in my opinion) the hardest part of any language, since their use is a feature that is characteristic/peculiar of each language. Therefore we will always have problems with them, since as far as I know in most cases there's no underlying logic, and no matter how fluent we become, we'll still ocasionally get confused. I even screw up in my own language when it comes to prepositions!
The only thing I could add is that I think something we could do is learn what are the typical phrases/words with which the most common prepositions combine.