From the article you linked:
ATF spokeswoman Deb Seifert told The Journal News on Thursday that she could not be more specific on the reasons LaGuercia’s license was revoked.
The ATF isn't saying. We won't know until they or the US Attorney's office makes more information public.
Apparently the license was revoked within a week of the Newtown shootings, and that's now permanent, following a 60-day period when the store owner could have appealed. The fact that he chose not to suggests that there may have been good reasons for the revocation, IMO.