When deploying a application to another environment, issues occur if your new version consists out of less modules then your old (already present on target environment). 

For example I tried deploying app that previously had 2  modules (A & B) connected to each other. In the new version it had only 1 module. (A) During the validation step it complained that the old version of B is not compatible with the new A.
Even though B should just be removed during deploy, seeing it's not longer part of our application.

This deletion should be picked up and handled by the deployment tool.