Not really. It happens by not drafting and signing enough talented amateurs in the first place. Once you do that well, once you stock your minor league system with many good prospects, you can trade some of them—even very good ones—for other players. Those trades only become “bad” if you don’t get good value back, or if you don’t have enough good prospects left in your system to fill a significant part of your major league roster. If you have a good minor league system in place, you can even withstand a “bad” trade or two and still have a good system.
If the Mets put in place a top front office that can collect talent in the minor leagues, a lot of these issues go away.. But they haven’t had that over the last several years, so I wouldn’t spend too much time stressing over the few, limited prospects that they have in their system at the moment.