Problem with pushing new commits to Merge Request

I’m using Gitlab Community edition provisioned by Cloudron.

We quite often have a problem with new commits pushed to a merge request. They are visible when you browse the branch view but they are not visible from the Merge Request view. and They not trigger CI jobs.

What might be the problem here? I guess this is somehow related to git push callbacks not being triggered properly. Is there a way to trigger them manually?

Thanks in advance.