According to MacRumors, Apple is currently working on the ability to merge multiple Apple IDs into a single ID. Currently those who have (for whatever reason) multiple Apple IDs are unable to merge them, even when contacting Apple support directly.
In an article posted yesterday however, it is revealed that a MacRumors reader had emailed Apple CEO Tim Cook and promptly received a phone call from an Apple executive relations employee regarding the issue. According to their account, the employee contacted the team responsible who said that they were aware of the issue and were concerned with iCloud exacerbating the problem. It was noted by the executive relations employee that they are working on it and in the meantime to pick a single account to use for all future purchases.
In an update to their article, MacRumors notes that a second reader has come forward, noting that they received a similar response over the issue. This prompt reaction by Tim Cook in responding to email from a customer is not his first and is consistent with his dedication to work.