I'm trying to optimise my queries but prefetch_related insists on joining the tables and selecting all the fields even though I only need the list of ids from the relations table.

You can ignore the 4th query. It's not related to the question.
Related Code:
class Contact(models.Model):     ...     Groups = models.ManyToManyField(ContactGroup, related_name='contacts')     ...  queryset = Contact.objects.all().prefetch_related('Groups') 
                Django 1.7 added Prefetch objects which let you customise the queryset used when prefetching. In this case, you'd want something like:
queryset = Contact.objects.all().prefetch_related(     Prefetch('Groups', queryset=Group.objects.all().only('id'))) 
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