Multi-layer graphs (e.g. multi-panel graph made by previous merging) were excluded in Merge Graph Windows Dialog.
The rule is improved in 2025b so that
If the multi-layer graph is within same rectangle frame, it will be included.
If all graphs are multi-layer graphs, so the number of graphs to include is 0, then all graphs will be included.
If the graph you want to merge is still not included in the dialog, please click > button in Graphs list box to manually add.