When you are making a fresh claim, the Home Office staff should take all the documents you provide, by way of supporting evidence. If you are making the application yourself, you should include a cover letter setting out all the documents enclosed.
Should the Home Office refuse to accept a certain document in your application that you consider to be relevant to your case, you should first speak to them. It is important that your case is looked at as a whole, and the person taking the documents will not be the decision maker.
You should also write a letter of complaint together with the supporting material that were not taken.
Always make sure that you have a copy everything you send, together with the date.