Sorry, I assumed by controlling packages your issue would be resolved. After a little testing with some dummy modules (you have yet to specify which modules you are using), I've verified you can suppress the warning assuming it is resulting from uncontrolled exports from the modules. Since A.pm is exporting twice, you can prevent it from exporting any subroutines when you use it explicitly by modding your use statement to:
use A qw();
yielding a final code
use A qw();
use B ;
#.... do something