My personal opinion is that it breaks history and CI tests for all the feature branches. But at GitLab we encountered customers that insisted on having a linear history after migrating from SVN. Therefore there is a function in the UI of GitLab EE to rebase a merge request when accepting the merge request. See http://doc.gitlab.com/ee/workflow/rebase_before_merge.html
The results from previous CI runs are no longer connected to the rebased commits, and most people don't have CI set up to retest each commit individually after a rebase.
I've never found this to be an actual problem in practice.