This happened to me when I published two APKs (versions 3 and then 4) in a short space of time. Clicking "Deactivate" on the dropdown next to version 3 appeared to fix it.
My guess is that this is a very-poorly-worded error message meaning something like "your original APK hasn't been published to all the update servers yet, so some of them may miss that version entirely". But it's a bit of a guess.
For some reason when you upload a new APK without immediately clicking "publish" (you probably clicked save draft the first time), Google thinks you want to publish BOTH apk at the same time.
This is usually needed when you have multiple APK for different configuration (say: a version for android 2.x and another for 3+ or a version for tablet and another for handset etc...)
However in your case you are just uploading an upgrade and you want it to replace your previous APK.
To solve:
The Google warning is missleading. Hope this clarify it.
I have solved the same problem with my app. I must upload from version 1.0 to the version 2.0. - I have uploaded the v2.0 in Beta. - When it was uploaded, I have DEACTIVATED the v1.0 in the PROD. - Next step was to MOVE the v2.0 to PROD from the BETA. - Then, the PUBLISH button was activated to finish the process. I hope it helps.!
The solution of @Chris is right. But what the message really means is:
version1 and version4 has the same configuration: same API level, same screen resolution... bascially everything in manifest...
So this means any device can install version can install version4, too.
Now everything is clear: since version4 has higher versionCode, every devices will recieve the version4 instead version1.
There's no meaning still put version1 "in production" anymore. Under no circumstance any device would recieve this version. So you should "deactivate" it.
This may be a hack, but you can workaround this by doing staged rollout to 1-50%, then increase it to 100%.
This case the error message does not prevent publishing your app and also you don't have to deactivate anything.
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