Confirmed here with version 7.04 of ExtUtils::MakeMaker. Here's a simple script to reproduce the error. Anything after the .pm in the module name will do.

#!/bin/bash

mkdir -p lib/A
cat > lib/A/B.pm <<EOT
package A::B;
our \$VERSION = 0.01;
1;
EOT

cat > Makefile.PL <<EOT
use ExtUtils::MakeMaker;
WriteMakefile(
    NAME            => 'A::B',
    VERSION_FROM    => 'lib/A/B.pm'
);
EOT

ext=foo
touch lib/A/B.pm$ext
perl Makefile.PL
rm lib/A/B.pm$ext
make
[download]

Certainly seems like a bug to me.

Update: any file created anywhere within lib/ appears to trigger it.