The following reproducing steps are valid for branch version only, because in trunk Datasets currently are used for input in read elements.
0. Open WD
1. Add some read element into the scene (e.g. "Read sequence")
2. Add a few (2 enough) files in property editor's field "Input file(s)", but don't cancel editing (e.g. by pressing left mouse button on the scene)
3. Delete the element from the scene.
Current result: Message box about dividing file list into separate iterations appears.