Since you're using Test::Class, my guess is that you have a test where you claim to be running $X tests but are actually running three less than that number. Find the method those tests are skipped in and count the number of tests you're running and compare that to the number of declared tests. For example, this will generate a similar problem:

sub foo : Test(4) {
  ok 1, 'we will have three tests skipped';
}
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If you're generating tests iteratively then the skipped tests are possibly indicative of a behavioral change you should look into.