If you use Sencha Command tool to build ExtJs application like this:
sencha app build
and experience something similar to the following error
[ERR] [ERR] BUILD FAILED [ERR] com.sencha.exceptions.ExBuild: Mixed-Mode x-compile and microload markup is currently unsupported [ERR]
here is the solution for your problem. The problem is that there are two parallel places where you defined references to js, css and/or theme files. Open up index.html and app.json files from the root of your project and check if there are references to js, css in both files.
Solution is to simply remove all file references and theme definitions from app.json file and take care that all of them are defined in index.html file. After this, you can run build command again without errors.