The fact that when loading a .ddo file more tables than those expected appear, means that those tables have been saved somehow in the file itself.
When you saved the .ddo file over an existing .ddo file, a pop-up window like the one below should have appeared
+ Clicking on 'OK' is most of the times the wrong choice, because all of the current selected tables will be appended to the already existing ones in the .ddo, creating even duplicates. This is probably the case why your Table set is unexpectedly big.
+ Clicking on 'Ignore' is most of the times the right choice to make. In fact the previous Table set will be overwritten by the current one.