First issue: code quality
How do you:
this generated code?
The issue is the same for any generated code.That's why code generation tools are used only for simplistic tasks where the code is mostly boilerplate.
For example in .NET world, Visual Studio generates code for Windows Forms and is limited to positioning and customizing controls, but nothing technically challenging. In the same way, Entity Framework generates the mappings for the database, which means lines and lines of boilerplate, uninteresting, monotonous code.
Second issue: performance
This issue may be non-existent in some cases (or at least the slight performance impact is very limited by severe caching, and a few milliseconds spent by the server generating the files is outweighed by the gains in terms of time you spend writing code), but you still need to measure the impact to know exactly how is it affecting your application.
Third issue: lower interoperability
If the code is generated server-side using server side programming language, you won't be able to reuse the same code in websites powered by other programming languages. Moreover, even migrating to newer versions of the same framework may be painful.