Great question — answering as the UphillTech team:
This seems surprising to me. Though I am working with Analytics and have more than 100 properties registered under me, I did not face such problem. I am pretty much sure that the tracking code of 'Site B' must be somewhere on some of the pages of 'Site A'. If you can just share the links of both sites, I can help you identify the issue.
Full answer by Chaitanya Ambardekar: https://webmasters.stackexchange.com/a/129018 (CC BY-SA 4.0).
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