There was a controversy years ago when he started giving kashrus to DD, 7/11 etc in flatbush, which are open on shabbos and serve cholov akum
Interestingly nobody complains when the Vaad of the 5 towns is machshir the same establishments.
That being said, for all I know there are also other issues.
That wasn't the issue with DD. the problem was that the chof K removed their hashgocho and he put it on w/o even asking why they removed it. Incidentally it was because of employees using the microwaves for non kosher personal items.
At the time I heard from someone in kashrut that If chof K removes a hashgocho, even goyim shouldn't eat there. (I'm sure that statement was dripping with sarcasm, but take it for what it's worth)
Later on he gave the hashgocho at Jezebel, and allowed them to serve non mevushal wine.
Eventually they got rid of his hashgocho and changed the name to J Soho and brought on OU.