Нашел решение
Удалил из build.gradle модуля yandexmapkitlibrary такой кусок кода
sourceSets {
main {
manifest.srcFile 'src/main/AndroidManifest.xml'
java.srcDirs = ['src']
resources.srcDirs = ['src']
aidl.srcDirs = ['src']
renderscript.srcDirs = ['src']
res.srcDirs = ['res']
assets.srcDirs = ['assets']
}
// Move the tests to tests/java, tests/res, etc...
instrumentTest.setRoot('tests')
// Move the build types to build-types/
// For instance, build-types/debug/java, build-types/debug/AndroidManifest.xml, ...
// This moves them out of them default location under src//... which would
// conflict with src/ being used by the main source set.
// Adding new build types or product flavors should be accompanied
// by a similar customization.
debug.setRoot('build-types/debug')
release.setRoot('build-types/release')
}
и все благополучно заработало