Thank you very much for the additional information and the sample files.
The problem is that your diagram contains several vertical "Recueil" labels whose "Size" policy is set to "Fit Node Width". These labels result in the diagram bounds being much larger than your pool node. You need to remove those labels so the total bounds of your diagram coincide with the bounds of your pool node.
I suggest the following approach for finding the problematic labels:
- Open "Edit" -> "Find".
- Turn off "Use These Criteria" for all tabs except the "Node Labels" tab.
- On the "Node Labels" tab, set criterion "Select" to value "Text" and criterion "Text" to value "Recueil".
- Click "Ok". This will select one label with the specified text.
- If the selected label is vertical (i.e. its "Rotation Angle" is "270") and its "Size" policy is "Fit Node Width", delete the selected label; otherwise leave it be.
- Press F3 to select the next label that satisfies your search criteria.
- Repeat steps 5 to 6 until there are no more problematic labels.
When you are done deleting labels, use yEd's "Fit Content" action (see yEd's tool bar, 8th button from the right) to "verify" the result. If all the problematic labels are gone, "Fit Content" will result in a "tight fit" of your diagram in the visible area.