The main difference between an ishtmus and a tombolo is that the ishtmus is connecting two large pieces of land, be it two large islands, two peninsulas, or marge areas separated by water, while the tombolo is connecting a large piece of land with a small island.
The similarity of the two can be seen in that that they both have a part that is usually sandy, and it looks as a natural bridge or trail that is connecting two pieces of land, and that is what occasionally can make a confusion.