Yes, there are. "Stitching" a group of local inventories is not the same as a origin-destination inventory being available. Unless you want to pay individualy for each flight, instead of getting a singly priced fare from A to B thru as many C,D,E,F of your choosing, your method most likely is not necessarily going to return the ticket you want. Carrier A may want to sell a local Q fare from A to B and also a local Q fare from B to C. That doesn't mean that they want to sell a Q fare from A to C via B, as they can may be able to make more $$ selling the separate tickets. If you want from A to C, that fare must be available when requesting space from A to C, not from A to B and a separate request from B to C.

Because you find "local" inventory in the class you want on multiple individual legs, does not make it "phantom" if not there when requesting it for a set of connecting flights, it only means that inventory is there on the legs for the single segment price on each leg, but may (or may not) be there for a single price for the combined legs when booked as a connection.