Change those print calls to warn(). I'm guessing that those arrays are kept around because the closures were kept around and that both were eventually cleaned up during global destruction. You are always free to clear a variable with prejudice - use undef as a function. undef $nodes might give you some different results. (you already did that. Whoops).
That may still be a bug though but whether it is in the reference counting of $nodes' array or $sub's clusure I don't know. But then it isn't clear to me that it is a bug.
