The few things you've mentioned are really not good signs, this is definitely not a reputable breeder. Good breeders very rarely own both the sire and dam; BYBs are more likely to own both parents because it makes breeding more convenient. While owning both parents is not always a bad thing, it is DEFINITELY bad in this case because both dogs were kept in a pen outside and obviously neither of them have been paid much attention. If the owners had spent more time with the female hen she wouldn't dig out of boredom. And instead of TRAINING and EXERCISING the "naughty" male boxer, they got him a playmate (translation = LAZINESS). Also, if you weren't even invited to meet the adult dogs who WERE on the property then that is another red flag. Last but not least, the puppy with diarrhea. There is really no telling what could have caused it -- there could even be a reasonable explanation -- but I would assume the worst about this particular breeder. They are obviously breeding for profit, NOT to better the breed. I am willing to bet that they do not perform any genetic testing on the dogs they breed and considering the way they "care for" the adult dogs it would not surprise me if these puppies have already been exposed to disease.
Read through this site top to bottom.
Finding a Responsible Breeder
When you're ready to start looking for another breeder, start with your local boxer club. Most regional clubs have breeder referrals and may also list websites or contact information for their members. Don't assume that ALL breeders listed on the club site are reputable -- you should still ask lots of questions (and get GOOD answers) before you decide to purchase a puppy.
U.S. Boxer Clubs
Another great way to get in contact with breeders is to attend a dog show. Chat up one of the boxer breeders; if the breeder you talk to doesn't have puppies at the time, they will probably know of someone who does and may refer you to them.