This sounds like a bug report to me as well. However, it would be good to review the data first, but this is not the venue for an in-depth review of the problem. You can submit a bug report using the Apple Developer Bug Report web page - make sure to select the iTunesConnect product, then email me with the bug report number and I can ensure that it reaches the correct team.
The more difficult aspect of reporting this issue lies in providing a means to replicate the problem. The iTunes Production Support QA team will only process bug reports where they have an application binary and the instructions to use the binary that will provide the results which you've described. Of course you could provide applicationReceipt samples, but there will only be limited analysis and little action - that is until the QA engineers can see the problem happening live with an app. The reason for this requirement is to be able to see the server respond - which is key to understanding the problem. The iTunes Store server is the entity that is sending the contents of the applicationReceipt that is updated in the application. Seeing the server gather it's data to place in the receipt is important to analysing the problem.
The other thing is that the QA folks will start the test from the beginning - I wonder whether you have seen this problem with a new test user account.
A different way to approach this issue - why are you analzying the transaction numbers. The applicationReceipt is signed by Apple so modifying the receipt should not be possible, except by Apple. If the applicationReceipt is forwarded to your server, then passed to the appropriate verifyReceipt server and the contents are validated, then the in_app array should present a current purchase history of the user's in app purchases (at least current as the applicationReceipt)
rich kubota - rkubota@apple.com
developer technical support CoreOS/Hardware/MFI