sqlpackage.exe fails on SignalR objects
Again, the failure rate is like 1 out of every 10 runs, and no one is
manually removing these objects

Although no one is manually dropping these objects, it seems SqlDependency is used to detect database changes. SqlDependency creates/drops ephemeral objects so, if the application is running during publish with the with the /p:DropObjectsNotInSource=True option, the object might longer exist when the deployment script is executed by sqlpackage.
One option is to stop the application while the dacpac is published. You could also exclude the problem objects during publish (e.g. using the DoNotDropObjectTypes option).