In the logs I see tombstone warning threshold.

Read 411 live rows and 1644 tombstone cells for query SELECT * FROM ks.tbl
WHERE key = XYZ LIMIT 5000 (see tombstone_warn_threshold)

This is Cassandra 3.11.3, I see there are 2 sstables for this table and the
partition XYZ exists in only one file. Now I dumped this sstable into json
using sstabledump. I extracted the data of only this partition and I see
there are only 411 rows in it. And all of them are active/live records, so
I do not understand from where these tombstone are coming from?

This table has collection columns and there are cell tombstones for the
collection columns when they were inserted. Does collection cell tombstones
get counted as tombstones cells in the warning displayed?

Did a small test to see if collection tombstones are counted as tombstones
and it does not seem so. So wondering where are those tombstones coming
from in my above query.

CREATE TABLE tbl (
    col1 text,
    col2 text,
    c1 int,
    col3 map<text, text>,
    PRIMARY KEY (col1, col2)
) WITH CLUSTERING ORDER BY (col2 ASC)

cassandra@cqlsh:dev_test> insert into tbl (col1 , col2 , c1, col3 )
values('3','3',3,{'key':'value'});
cassandra@cqlsh:dev_test> select * from tbl where col1 = '3';
 col1 | col2 | c1 | col3
----------------+----------+----+------------------
              3 |        3 |  3 | {'key': 'value'}
(1 rows)

Tracing session: 4c2a1894-3151-11e9-838d-29ed5fcf59ee
 activity
                   | timestamp                  | source        |
source_elapsed | client
------------------------------------------------------------------------------------------+----------------------------+---------------+----------------+-----------

Execute CQL3 query | 2019-02-15 18:41:25.145000 | 10.216.1.1 |
     0 | 127.0.0.1
                  Parsing select * from tbl where col1 = '3';
[CoreThread-3]              | 2019-02-15 18:41:25.145000 | 10.216.1.1
|            177 | 127.0.0.1
                                                       Preparing
statement [CoreThread-3] | 2019-02-15 18:41:25.145001 | 10.216.1.1 |
         295 | 127.0.0.1
                                        Reading data from
[/10.216.1.1] [CoreThread-3]    | 2019-02-15 18:41:25.146000 |
10.216.1.1 |            491 | 127.0.0.1
                                Executing single-partition query on
tbl [CoreThread-2]    | 2019-02-15 18:41:25.146000 | 10.216.1.1 |
      770 | 127.0.0.1
                                              Acquiring sstable
references [CoreThread-2] | 2019-02-15 18:41:25.146000 | 10.216.1.1 |
          897 | 127.0.0.1
 Skipped 0/1 non-slice-intersecting sstables, included 0 due to
tombstones [CoreThread-2] | 2019-02-15 18:41:25.146000 | 10.216.1.1 |
         1096 | 127.0.0.1
                                 Merged data from memtables and 1
sstables [CoreThread-2] | 2019-02-15 18:41:25.146000 | 10.216.1.1 |
       1235 | 127.0.0.1
                                    Read 1 live rows and 0 tombstone
cells [CoreThread-2] | 2019-02-15 18:41:25.146000 | 10.216.1.1 |
    1317 | 127.0.0.1

  Request complete | 2019-02-15 18:41:25.146529 | 10.216.1.1 |
  1529 | 127.0.0.1
[root@localhost tbl-8aaa6bc1315011e991e523330936276b]# sstabledump
aa-1-bti-Data.db
[
  {
    "partition" : {
      "key" : [ "3" ],
      "position" : 0
    },
    "rows" : [
      {
        "type" : "row",
        "position" : 41,
        "clustering" : [ "3" ],
        "liveness_info" : { "tstamp" : "2019-02-15T18:36:16.838103Z" },
        "cells" : [
          { "name" : "c1", "value" : 3 },
          { "name" : "col3", "deletion_info" : { "marked_deleted" :
"2019-02-15T18:36:16.838102Z", "local_delete_time" :
"2019-02-15T18:36:17Z" } },
          { "name" : "col3", "path" : [ "key" ], "value" : "value" }
        ]
      }
    ]
  }

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