Absolutely nothing. Containers are great and play many important roles in computing, especially in development and security.

There are problems with the way some people use them, however. As is often the case, containers have become a solution looking for problems. Many people use them because they think it's "cool" or because it's a path of least resistance.

In scientific computing, containers are often used to isolate badly designed or badly implemented software that is otherwise difficult to install outside a container. For example, software build systems that bundle share libraries can cause conflicts with other versions of the same shared library.

Isolating such software in a container will get it up and running and work around conflicts, but with some major down sides:

Misusing containers in this creates more disorder and complexity where there is already too little IT talent available to manage things well.