When copying Persian text there are squares with numbers inside

This squares are called TOFU and are placeholders since there's no glyph available in your system that matched the copied glyph from the PDF. Keep in mind: There are thousands of languages and much more glyphs used out there in the world. Depending on the font your're using and its coding it can hold information for say 128 characters (ASCII) or 65.536 (UTF-8). This is only in theory. It also depends on which characters the designer of the particular font has embedded into the font file. Free fonts often only contain the typical ASCII characters used in english speaking regions. Other characters that may be used in Europe or Asia are often missing. There's propbaly nothing you can do about this in Reader.