If you are using PermissionsDispatcher library thn its mentioned as issue for duplicate class entry.
How to Check attached libraries Dependency/hierarchy ? which causes duplicate entry for libraries.
In your case you need to make changes as per mentioned in libraries known issue.
compile 'com.github.hotchemi:permissionsdispatcher:2.0.3'
compile 'com.github.hotchemi:permissionsdispatcher-processor:2.0.3'
Make changes as per below
compile 'com.github.hotchemi:permissionsdispatcher:2.0.3'
apt 'com.github.hotchemi:permissionsdispatcher-processor:2.0.3'
For more details on duplicate entry issue please check this
UPDATE
Its required to define apt dependecies in root level build.gradle
file also
check this for root level build.gradle file declaration.
Let me know if anything