Hello!
Normally that would not happen as JRebel does not touch Emac functionality at all. Though when you do updates via Eclipse Marketplace, it by default contacts all update sites which might lead to undesirable additions. For the future you can disable it by unchecking “Contact all update sites” on the buttom of update window where it gives you options of what you are uploading for a particular plugin.
Hope it helps!
Kind regards,
Valerie