Even if the script is written as vanilla CGI, if it's being run on apache with mod_perl, there are a couple ways that it could be set up to optimize performance by caching CGI scripts to avoid having to reload and recompile them every time they're referenced.

By default, apache request-handling processes kill themselves after handling 50 requests, at which point their cached data is lost and the replacement process reloads everything. I suspect that the two anomalous log entries were the result of a process which had previously handled requests for your old script and didn't notice that there was a new version. By now, though, it is long dead and you shouldn't see any artifacts of the old version in the future.