I have a similar problem when I was testing out the Google Sample code found here https://github.com/GoogleCloudPlatform/gradle-appengine-templates/tree/master/GcmEndpoints and What XYZ said really helped me resolve this issue.
I was able to send the messages to my phone from my google app engine API Explorer under the messaging.messagingEndpoint.sendMessage method however in the google app engine console logs, it always said MismatchSenderId. The error logged when clearly there was not supposed to be an error bugged me.

I was really confused and here is how I managed to resolve this:
- Uninstall your android app from your phone.
- Reinstall your android app and take note of the reg ID.
- Go onto API explorer under Services > registration API v1 > registration.listDevices and list all your RegID for GCM.
- Copy this list somewhere - to notepad.
- Go onto API explorer under Services > registration API v1 > registration.unregister and unregister all the regID that does not match to the one used by your app.
Retry sending the message and this time it should work without the error being recorded in the google app engine console logs.