we notice that when we deploy a certain deployment slot, not all instances serve the same version

The reason you're facing this issue is due to ,

• Some instances do not pick up the new deployment due to Azure's load balancer keeping them active with the old version.
• If ARR Affinity is enabled, some users may remain stuck on old instances.

To resolve the issue ,

1. Disable ARR Affinity:

Go to Azure App Service -> Configuration -> General settings -> set Session affinity ans session affinity proxy to off.

This will prevent from being stuck on old instances.

2. If using slot swapping, enable Swap with Preview to ensure all instances are warmed up before swapping.

Thanks @ruslany for clear explanation, refer this Blog to learn how to warm up Azure Web App during deployment slots swap.

3. Add the below setting in environment variables section of your Azure App Service.

This ensures that instances are refreshed following a deployment.

Please refer this MSdoc for better understanding of the above environment variable setting.