There is no difference.

I suspect what your source might be referring to is this conspiracy theory which says that there's an "American civil flag" which is different than the "military flag" which is normally flown. These conspiracy theorists then go on to say that the "American civil flag" has been suppressed by the government in an effort to bring us all under martial law.

In actuality, the "civil flag" they're speaking of is a variation of the US Revenue Ensign, which was adopted solely for the use of the Coast Guard and the Customs Service. Other executive departments also have their own flags, for use inside the department and to mark their respective posts. Meanwhile, the standard United States flag, with thirteen horizontal stripes, has been since the beginning intended for use everywhere as a symbol of the nation.