Is the same happen to the native speakers when they were learning there own language?
I'll take this opportunity to 'reprogram' a part of your grammar. If you want to take my suggestion, type this sentence 3 times and ready it aloud slowly 3 times:
Does the same thing happen to native speakers?
By repeating that sentence over and over again, you'll build your 'sense' of correct grammar. Grammar is knowledge so internalized that it must become automatic, like something you 'sense' rather than like rules you memorize.
I agree that it's annoying when words sound the same but have different spellings and meanings. But it's important to know that you do not need to have perfect English in most situations -- only perfect focus and good intentions. Modern people know that many of the smartest professionals are the ESL professionals.
My idea about the hardest part of English: Conjugating verbs. That might be the hardest part of any language. And it's another challenge you can overcome if you listen to excellent English, read excellent English aloud, and actually practice typing sentences you find in great books or hear on television, etc.
Here is an example of a great way to practice:
You can collect great sentences, practice them, and modify them by replacing different words. (Repeat this sentence 3 times)
Now modify the sentence:
You can collect the web addresses of a few websites that offer English editing, contact them, and ask them to review your writing. (This is an example of a sentence with the same structure as the sentence above, but the words are changed to give it a different meaning).
Practice several sentence structures you like! : )