chrom from NCBI not getting all the intervals

[conchoecia]

Sometimes, the interval for the proteins in the genome are incorrect. For example, in this example for the Hydra genome available on NCBI:

              protein         scaf strand     start      stop  length
3      XP_047134143.1  NC_061156.1      +    107132    112407    5275
11     XP_047139822.1  NC_061156.1      -    185093    236530   51437
19     XP_047143191.1  NC_061156.1      +    341267    341267       0
45     XP_002157336.3  NC_061156.1      +    828243    829411    1168
69     XP_047135734.1  NC_061156.1      -   1458157   1458157       0
...               ...          ...    ...       ...       ...     ...
32555  XP_047124590.1  NC_061170.1      -  39819170  39891048   71878
32574  XP_047125113.1  NC_061170.1      +  40367776  40431694   63918
32577  XP_047125116.1  NC_061170.1      -  40453082  40453301     219
32594  XP_047124346.1  NC_061170.1      +  41062208  41062612     404
32607  XP_012553780.2  NC_061170.1      +  41498303  41498303       0