welcome to the KNIME forum!
From what you describe, I think I understand the problem, but it is difficult to help you. It is best to share a small workflow where the problem occurs, or if that is not possible, a screenshot of the settings dialog of the node that causes problems. Currently, I do not know which loop nodes you are actually using (there are several), but let me give it a try.
If you use the Loop End node, you can tick the box at “Ignore empty input tables”. Does this help?