The only other thing I can guess you might have done to get this behaviour is to override the permissions for a single stage
within a pipeline to allow it to be triggered by only user1 via PipelineConfig > stage > permissions.
Normally this is intended to restrict (manual) stage approval triggers to a different group than the overall pipeline as documented at https://docs.gocd.org/current/configuration/dev_authorization.html#adding-authorization-to-approvals
. If you are configuring permissions for a pipeline stage
, you may be doing it in the wrong place to get your desired behaviour. Generally the "pipeline group" is the normal unit of permissioning within GoCD and stage-specific permissions are used for special cases.
Since pausing as an operation is at the overall pipeline scope (not for a specific stage), the permissions need to be restricted from the pipeline group which the pipeline belongs to.
If you still think something is not working as expected, perhaps share your configuration of the pipeline group and the pipeline stages, and share some more details/screenshots etc so someone else can reproduce what you are seeing.