Yip, that whole MySejahtera thing is a nightmare.
It was best to register through their alternate web portal first, not phone app with QR screenshot of vaccines. I had to reach out to them on twitter as their phone app support was awful.
I had to get them to complete it also on arrival....utter mess vs thaipass before.
Usually tech savvy, the Malaysia app was a brickwall for me.
Here is website interface - faster.
https://www.mysafetravel.gov.my/application