JPA Rough Spots

While JPA is nice, here are some possible rough spots:
TOPLINK-60
Some foreign key columns will confuse TopLink JPA provider off in LAZY fetch mode, causing TOPLINK-60 exception that complains mysteriously about a missing method. Apparently the cause is related to some complicted 'weaving' logic. Quick fix is to switch to EAGER for the offending column (use missing getter method name as hint) and deal with consequences later.
Uncommitted Persist
Persisted but not yet committed POJO instances don't really exist which could lead to problems when you reference them from other POJO instances. Fix is to fiddle with CascadeType settings. For example, if A and B are both new instances and A.b references B, then make sure A.b cascade type is set appropriately (i.e. CascadeType.ALL) then just persist A. Since A.b is set to cascade, persisting A will cause B to be inserted first then its surrogate primary key will be used to insert A. If A and B has a OneToMany relatiohship then you would use A.getB().add(b) instead of A.setB(b).
Frankly, I don't like all this behind-the-scene cascading business so I try to avoid using it whenever I can. But it's difficult to avoid during inserts as the only alternative I can see is  brute-forcing commit and fetch at each step and deal with rollback manually.