How acidic waters make rocks disappear?
First of all, the rocks do not disappear they dissolve, so they are still there only dissolved into the liquid.

You are using an acid (vinegar), this has a low pH.

The rocks you are using (limestone) they have a high pH (alkaline).

The alkaline rock you add to the acid will dissolve but only until the acid is neutralized. The reaction stops when the pH reaches close to 7,0.

If you had used less limestone or more vinegar the rock will be fully dissolved but the pH of the liquid will stay low. To neutralize the vinegar you must then add more limestone.

So you did nothing wrong except maybe using too little acid.

I will stop my answer here, but if you had taken this reaction one step further you would have made marble (the bubbling you might have seen was carbon dioxide CO2).