it is very possible that you turned off construction history at some point. if construction history is off then combine will not create any utility nodes. and the same is the case for many operations. but maya uses the history and utility nodes in a smart way. it uses them to eliminate many recalculations and duplications…
When you combine two or more meshes in maya it creates a group for the new geometry and then reference groups based on the old geometry. You want to make sure after you combine meshes together you delete history, then go into the outliner and delete the groups that you don't need. Also make sure you remove any meshes from…