"Do you see train stations often?"
Translation:Gyakran látsz vasútállomásokat?
That would make it a different sentence.
"Gyakran látsz pályaudvarokat?" - "Do you often see train stations?" / "Do you see train stations often?"
"Gyakran pályaudvarokat látsz?" - "Is it train stations that you often see?"
The emphasis, and the relationship between the words, is different.
Well, the word order is indeed flexible, but it does not mean that there is no reason behind it. :) It is just one more tool in the box that we can use to express different ideas. Other languages, with more restrictive word orders, might need to rely more on verbal emphasis. I frequently see words set in italic in English language books, to indicate where the emphasis is. There is no need to do that in Hungarian, because the word order usually takes care of it perfectly.
Yes, maybe there could be more emphasis on teaching the significance of word order. Until then, you can come to these discussions and ask all you want. Somebody will try to help you. These comment sections are full of discussions on word order, you can keep reading them.
Also, listen to the audio as much as you can. Since it was recorded with a real person, the emphasis and intonation are all correct. It may help you to pick up the nuances. But give yourself plenty of time, I can imagine there is so much to adjust to with Hungarian. These things do need time to process.