Hi. I just tried reproducing this and wasn’t able to do so. I tried with standard objects (Account), custom objects, and Tooling API objects, and in all cases (for me), SEL* generated a valid query without the relationship targets included.
Specifically what kinds of queried objects are resulting in this behavior for you? Can you try using File | Invalidate Caches and see if the behavior persists after restarting and reindexing completes?
Regards,
Scott Wells