Seeing tombstone warning message

We deleted data for some of the rows in one of the column families.
After that we ran repair on all nodes, and followed by reducing gc_grace_seconds that way compaction can remove all the tombstones upon expiry of gc_grace_seconds time.

When we are querying the data now, seeing the following errors:
WARN [ReadStage:1142] 2015-05-06 17:50:53,602 SliceQueryFilter.java (line 231) Read 1 live and 1487 tombstoned cells in XXXX (see tombstone_warn_threshold). 10001 columns was requested, slices=[-], delInfo=

We deleted this data while back and for sure gc_grace_seconds is elapsed long time back and we use leveled compaction. In the above, errors, localDeletion points to some time in future (MAX INT VALUE) and that could be the reason these are n't being purged. Any help (or) workaround is appreciated.