var pipeline = {};
// (...) adding things in pipeline

for(var key in pipeline) {
  fs.stat(pipeline[key].path, function(err, stats) {
    if (err) {
      // clear that one
      delete pipeline[key];
      return;
    }
    // (...)
    pipeline[key].count++;
  });
} 

The problem is that there is only one instance of var key. All callbacks will share the same key instance. At the time the callback will fire, the key will most likely have been incremented and not pointing to the element we are receiving the stats for.

var pipeline = {};
// (...) adding things in pipeline

var processOneFile = function(key) {    
  fs.stat(pipeline[key].path, function(err, stats) {
    if (err) {
      // clear that one
      delete pipeline[key];
      return;
    }
    // (...)
    pipeline[key].count++;
  });
};
    
// verify it is not growing
for(var key in pipeline) {
  processOneFileInPipeline(key);
}

By creating a new function, we are scoping key inside a function so all callback have their own key instance.