I can duplicate this behavior. Probably a bug. Only alphanumeric characters and dashes are allowed in tag slugs, so my slugs for C++ and C# were created as “c” and “c-2,” respectively. Adding these tags to a new post by name rather than slug lumped them all into C#. (Or was it C++? Either way, they evaluated to the same.)
Manually updating the slugs to “cpp” and “csharp” worked around the bug in my install. Have you customized your tag slugs, or are they “c” and “c-2?”
Update: taxonomy.php does check that the slug matches before checking the full tag name, and they both evaluate to the same slug (“c”), hence the incorrect match.
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