We came across the following JQL query (which admittedly is not very useful as usedBy is actually mappedBy=uses - but I guess this can be reproduced with more useful ones) which starting with some changes in 5.2.3-5.2.4 (cannot really test 5.2.3 as this is broken for another reason) produces an query that derby considers invalid, although I'm not exactly sure why - Derby bug? The trigger seems to be that the inverse relation join now is replaced by a subquery.
Results in SQLSytaxErrorException:
Column 'ABSTRACTCO4_.ID' is either not in any table in the FROM list or appears within a join specification and is outside the scope of the join specification or appears in a HAVING clause and is not in the GROUP BY list. If this is a CREATE or ALTER TABLE statement then 'ABSTRACTCO4_.ID' is not a column in the target table.
Query in 5.2.2:
Apache Derby 10.13.1.1 (10.12.1.1 also)