When using pt-table-checksum to verify replication between a master and slave, I found that there were certain tables that were not being checksummed with the following message:
Aborting <table> because <index> cannot be nibbled safely.
Curiously, this table did have a UNIQUE index (in fact, the one in use here), but it was still being skipped. I output a trace and ran pt-table-checksum again to see which index was failing, and it turned out to have been the right one:
Aborting <table> because <index> cannot be nibbled safely.ID ne id
So it seems that when an EXPLAIN is run on a query, it grabs the index in whatever case it's in, but at some point during the initialization/execution of the nibble iterator, the index is lowercased. Then, when verifying the next nibble, the string comparison done is case-sensitive, so "ID" does not match "id" even though (a) it's the same index and (b) MySQL indexes are case-insensitive anyway.
There was another point later on that would verify the right index was used that had the same issue; I patched that as well.
The enclosed patch fixes the issue for me.
Thanks for reporting this and providing a patch. I'll write a test case and fix the code.