I had a cruiser and 3 destroyers that I was trying to merge. Together they would be 13/16 or 14/16 logistics points. I had just merged an identical fleet a few seconds earlier but the second one of identical type ships would not merge. The three destroyers were stacked as a 9 and the the cruiser was a 4 or 5 on its own. I think it merged previously and then came undone after the first move I did with it. The second time I moved it it came apart as a 9 and 4 and would not merge.

One thing I didn't try is disbanding the destroyer portion of the fleet and merging them again one by one... however you should not have to do this.