When you filed the 501c3 application, was it written from the standpoint of 3 unique groups, or did that split occur after you earned the 501c3? You might be able to politely suggest that the other groups, now that they have grown to such a size, should file their own 501c3 --- and you'd be happy to help them do it.
What are they doing that has you so concerned? Granted, if they stay under your tax id number, you'll need to have their financial information so you can do a consolidated report on your annual Form 990. That alone might be reason enough to separate. And technically, if all 3 groups share the same tax id #, they all share all the money.
When our PTSO formed, we were one school, but our area is growing (too fast) and we are now 3 with another slated to open in August and another after that. We filed our 501(c)(3) status as a District PTSO, now we are wondering if that wasn't a HUGH mistake. We are untrusting of the newest school and the things we have been hearing they have done. We fear them causing us to lose this status we value so greatly.
We are wondering if there is anyway way for us to separate ourselves from the other 2 schools. We are the ones who filed the paperwork and paid the money, though one of the schools did re-imburse us 1/2 of the fee. The schools just seem to think that because they are part of the district now, they are permitted to use our tax-exempt number. No one even asked us if they could use it, they just assume.