They currently result in contradictions where clauses such as: c.id = 1 and c.id= 2 are generated.

This could be resolved in two different ways:

Multiple jointures (one per clause)

join c as c1 join c as c2 where c1.id = 1 and c2.id = 2

The disadvantage is that we do not control the process that produces the jointures when generating the restriction clause, so it will require significant changes.

Subqueries

where id in (select id from Entity e join e.c where e.c.id = 1) and id in (...)

Advantage: clauses are contained and likely easier to generate.

Drawback: the context to refer to aliases in the root query is not available.