Without seeing your SQL statement, it is difficult to say. However, left joining on key-constrained columns shouldn't be an issue so long as the primary key is in the left table.
http://dev.mysql.com/doc/refman/5.0/en/example-foreign-keys.html
If the primary key is in the right table, then you might get unintended results.
Suppose you have TableA with A_ID as a primary key and TableB with B_ID as a foreign key for TableA A_ID. This should return all records in TableA and matching records / nulls for TableB:
SELECT TableA.A_ID, TableB.B_ID
FROM TableA
LEFT JOIN TableB ON TableA.A_ID = TableB.B_ID
However, the following would only return all records in TableB, with no nulls because the key constraint would prevent TableA from having records that aren't in TableB:
SELECT TableA.A_ID, TableB.B_ID
FROM TableB
LEFT JOIN TableA ON TableA.A_ID = TableB.B_ID
The following would also return only those records that are in TableB:
SELECT TableA.A_ID, TableB.B_ID
FROM TableA
LEFT JOIN TableB ON TableA.A_ID = TableB.B_ID
WHERE TableB.B_ID IS NOT NULL
And depending on any groupings you are using, you might get bad results. There are other possibilities, but without seeing your syntax and data, I can't tell.