Do you have a dependency loop? If Perl starts compiling your script and encounters a line like this:
use PackageA;
Perl pauses the compilation of your script; locates PackageA.pm and starts compiling it. If it encounters a line like this:
use PackageB;
Perl pauses the compilation of PackageA; locates PackageB.pm and starts compiling it. Normally, that would complete successfully, and Perl would go back to complete compiling PackageA and when that completes successfully it would go back to compiling your script and when that completes successfully it would start to execute the compiled opcodes.
However, if PackageB.pm contains this line:
use PackageA;
You might expect it would do nothing since Perl has already processed PackageA.pm but the problem is that it hasn’t finished yet. So Perl will pause the compilation of PackageB and start compiling PackageA.pm again from the beginning. That could trigger the message you’re seeing about subroutines in PackageA being redefined.
As a general rule, two packages should not both depend on each other. Sometimes however the loop is harder to locate because it is caused by a third package.