Why does a syntax error occur when running a recompiled mobile app?

Question

Android

I decompiled the apk using apptools, compiled the resulting apk, signed it, and when the application is launched on the phone, a package parsing error occurs, what could be causing it? Because of a broken apk? Perhaps because when decompiling there was a folder "unknown files". Or because of the signature? Well, I don't think she has anything to do with it. So if an application, during decompilation, already produces files that are not suitable for compilation, then how can such an application be debugged at all, because for debugging you also need to add an item to the manifest? Is it even possible to debug such an application?