BUG: outer merge with indicator
# Inconsistencies of pandas merge

I tried to do an outer merge two dataframes and I observed that `left_only` values are missing but if I take a subset of those data `left_only` values appear

unfortunately I am not allowed to share those data and I have not yet found a minimal test case

**From full dataset**
```

(Pdb) outer_full = pd.merge(left_df, right_df,how='outer',on=['start', 'stop', 'reference', 'alternative'], indicator=True)
(Pdb) outer_full[outer_full['sequence_id_y']=='something']
         start   stop   reference alternative                           sequence_id_x    sequence_id_y      _merge
886      23604  23604           C           A  sample_of_interest  something        both
63840     8512   8512           A           G  sample_of_interest  something        both
65224    28270  28271          TA           T  sample_of_interest  something        both
124138   28111  28111           A           G  sample_of_interest  something        both
182893   27972  27972           C           T  sample_of_interest  something        both
241900     913    913           C           T  sample_of_interest  something        both
299398   18171  18171           C           T  sample_of_interest  something        both
300613   21990  21993        TTTA           T  sample_of_interest  something        both
358445    9190   9190           G           T  sample_of_interest  something        both
359600    6954   6954           T           C  sample_of_interest  something        both
418297   28282  28282           T           A  sample_of_interest  something        both
476408   23063  23063           A           T  sample_of_interest  something        both
541127     241    241           C           T  sample_of_interest  something        both
815175   28977  28977           C           T  sample_of_interest  something        both
874649   23709  23709           C           T  sample_of_interest  something        both
934071   11287  11296  GTCTGGTTTT           G  sample_of_interest  something        both
995638   24914  24914           G           C  sample_of_interest  something        both
1054348  28280  28280           G           C  sample_of_interest  something        both
1112331   5986   5986           C           T  sample_of_interest  something        both
1171810  28281  28281           A           T  sample_of_interest  something        both
1229819  14676  14676           C           T  sample_of_interest  something        both
1478469  21764  21770     ATACATG           A                                     NaN  something  right_only

```
**subset**
```
(Pdb) outer = pd.merge(left_df, right_df[right_df['sequence_id']=='something'],how='outer',on=['start', 'stop', 'reference', 'alternative'], indicator=True)
outer
    start   stop   reference alternative                           sequence_id_x    sequence_id_y      _merge
0   23604  23604           C           A  sample_of_interest  something        both
1    8512   8512           A           G  sample_of_interest  something        both
2   28270  28271          TA           T  sample_of_interest  something        both
3     705    705           A           G  sample_of_interest              NaN   left_only
4   28111  28111           A           G  sample_of_interest  something        both
5   29442  29442           A           G  sample_of_interest              NaN   left_only
6   27972  27972           C           T  sample_of_interest  something        both
7     913    913           C           T  sample_of_interest  something        both
8   18171  18171           C           T  sample_of_interest  something        both
9   21990  21993        TTTA           T  sample_of_interest  something        both
10   9190   9190           G           T  sample_of_interest  something        both
11   6954   6954           T           C  sample_of_interest  something        both
12   5264   5264           A           G  sample_of_interest              NaN   left_only
13  28282  28282           T           A  sample_of_interest  something        both
14  23063  23063           A           T  sample_of_interest  something        both
15    241    241           C           T  sample_of_interest  something        both
16  28977  28977           C           T  sample_of_interest  something        both
17  23709  23709           C           T  sample_of_interest  something        both
18  11287  11296  GTCTGGTTTT           G  sample_of_interest  something        both
19  24914  24914           G           C  sample_of_interest  something        both
20  28280  28280           G           C  sample_of_interest  something        both
21   5986   5986           C           T  sample_of_interest  something        both
22   1438   1438           T           C  sample_of_interest              NaN   left_only
23  28281  28281           A           T  sample_of_interest  something        both
24  14676  14676           C           T  sample_of_interest  something        both
25  21764  21770     ATACATG           A                                     NaN  something  right_only

```