You're on the right track and your gut told you this was wrong. It is very wrong.
Providers of the same group are considered inclusive as part of the global surgery package. You should not be billing an E&M post-operatively for these patients who continue to be in the global period for surgery done by the physician of the same group, unless the E&M is separately identifiable....meaning different problem, not different provider or common post-op complication. It doesn't matter if billing incident-to or not....the NP cannot bill during the global period for patients in your same practice for post-op care. One of the reasons surgeons use mid-levels is that they can handle the unbillable post-op services, freeing up the surgeon's time. From a patient care perspective, the surgeon should be making the decision for surgery, whether or not the -57 is appropriately used. Arbitrarily using the -25 and -57 to override claim edits is considered questionable (I'm not going to use the 'F' word here) business practice.
My advice is to immediately contact your payers and refund the money that's been billed separately during the global period, and then create a coding/billing policy to outline the correct way to bill these. If your surgeon/NP disagrees and directs you to continue to bill this way, get yourself a new job. You've unbundled these surgeries, which is high on the OIG's workplan (always). Then read through the instructions for the CCI edits, as well as the introduction in CPT's surgery section, and the information on modifiers. Then get yourself to some coding/billing training with regards to surgical coding. You shouldn't be tackling this without a solid understanding of surgical coding.