[SalesForce] Didn’t understand relationship ‘opportunity__c’ in field path

based on the select part of your query it appears that addresses is a child of account, in which case, your where clause don't make any sense. you probably want some kind of semi-join type query, e.g.

select .... from account where id in (select accountId__c from address where city__c like :term)

You have to use the child relationship name. You can always find it by using a script like the following:

for (ChildRelationship relation : SObjectType.Contact.getChildRelationships())
    if (relation.getChildSObject() == AccountContactRelation.sObjectType)
        system.debug(relation.getRelationshipName());

Paste the relationship name verbatim into your subquery, rather than the child object name.

Notice that you have two FROM clauses:

Select Email, Id, (Select ContactId, AccountId From AccountContactRelation) From Contact

In your subquery, you need to use the relationship name. In your top level query, you need to use the API Name of that SObject. Change AccountContactRelation to AccountContactRelations and you query should compile.