Lookout regularly checks for any changes made to your contacts.
Google automatically creates and manages contacts in your Gmail account, and Android imports and updates them on your phone because the contacts are associated with that Gmail account.
It's entirely possible that an adjustment to one of Google's contact management policies can be responsible for a "change" (e.g. a contact could have been relocated from one group to another), which would be perceived by Lookout as a deletion if both contact groups are not synced to your phone. In that case you would be notified even if you hadn't actually modified the contact yourself.
Normally Google makes these changes silently, but because Lookout is regularly checking for any change made to a contact—so that your Backup will always be up-to-date—we report the change even if Google doesn't. We don't track the set of changes to your data; we only report that there is a change.