the 501 is only a "tax" status and has really nothing to do with how the "facility" is being run.
If you feel the animals are not being cared for properly, contact animal control. Missouri has really been stepping up to try and help the animals (the new laws are supposed to help control some of the puppy mills and such).
You can also call the Missouri Humane Society (or email them) and ask them.http://www.hsmo.org/
They have a section on their website about how to report neglect or abuse.
Of course, I'm assuming this 501 is in Missouri.