I think they are size restrictions, CJ posted about the process I think.
Does this help?
'Supporters may bring a flag into the ground WITHOUT permission from Wembley Stadium if:
The flag is smaller than 250cm in size at the widest or longest point.
It does not have an attached flag pole
In the case of an attached flag pole, it is made from wood and plastic only and is no longer than 1 metre in length and 1cm in diameter.
There is no advertising or commercial message on the flag
It does not contain any abusive or defamatory message
**Please note that flag poles made of metal are not permitted inside the stadium, no matter what size or length the flag / pole is.
If a supporter arrives at Wembley Stadium and their flag does not come under the above points, and they have not gained permission from Wembley Stadium, the flag may be confiscated at the turnstiles and not allowed into the Stadium.'