Here are a few examples of Internet Exchange Point business alignment clashes:
A large network-savvy content provider installed at the JPIX peered openly. The provider requested a cross-connect to another ISP in the building. The colocation provider refused since it might adversely impact its business by bypassing it. (KDDI owns the building and KDDI also sells transit.)
Another example of a business alignment issue is MAE-East. In the late 1990's, WorldCom, a large ISP at the time, owned MAE-East, a large IXP on the east cost of the U.S. Building into MAE-East supported a competitor (WorldCom) and required purchasing WorldCom circuits. Peering at MAE-East meant paying money to your competitor, supporting its peering business, and reinforcing its position as a central component of the Internet in North America.
Finally, in the days of Exodus (the company), upper management sign-off was required for any in-building cross-connects within its data center. Too many hosted companies were bypassing the Exodus network, so Exodus felt it was missing out on a transit revenue opportunity with every cross-connect run within its building.
The fact that the colocation company can see who comes and goes was also raised as a concern to some ISPs. If your competitor gets to see all of your prospective customers, that competitor is in a position to offer its services directly. These issues are the types of issues that come up in discussions on the topic.
ISPs prefer an IXP that is not owned or operated by a competitor.