When you have Report A, and a subreport, report B.
Put twice a 'subreport' in report A, and reference both to report B (path could be like "subreps/reportB.jasper")
Upload to server, execute report: Exception is thrown.
It appears that Jasper only converts the first expression to "repo:reportB.jasper" and leaves the second one untouched... (So it's subreps/reportB.jasper, which throws the exception "can't find subreport in directory subreps/reportB").
I use JapserStudio 6.0 but same problem occurs with 6.2. We are on server 6.0