Reproduction steps:
1) Download and open user's attached project
2) Try to 'build and run' "EmptyScene" scene on any Android device
-- Notice that build fails with error: "Unable to convert classes into dex format. See the Console for details."
3) Press 'Ok' button
-- Notice that Unity still tries to push application to the device ignoring previous build error.
At the end throws this message:
"Unable to install APK to device. Please make sure the Android SDK is installed and is properly configured"

Expected result:
Unity stops building project as soon as error appears.

Regression appeared in 5.5.0p4

Reproduced with:
5.6.0f2, 5.6.0b1, 5.5.2p4, 5.5.0p4

Unable to reproduce with:
5.5.0p3

Issue has been fixed in 2017.1.0b1 and backported to 5.6.0p1 and 5.5.3p1

However using the shortcut to build (CTRL/CMD + B) still reproduced the issue.