In general, see How to describe CDS feature, when termination codon is found in the range.
You can also see Protein Coding Sequence; CDS feature to describe CDS feature.
Following items are case study for the error.

  1. Did you correctly specify /codon_start qualifier to indicate reading frame of the CDS feature?
    Select 1, 2 or 3, appropriately.

    References:
    Offset of the frame at translation initiation by codon_start
    How to fix error message: “First codon [***] is not a start codon.” / “Final codon [***] is not a stop codon.”? How to fix error message: “Value of [ codon_start ] is not 1, but [

  2. Have you specify correct genetic code for /transl_table qualifier?
    See followings and specify genetic code, appropriately.

    References:
    The Genetic Codes
    About /transl_table qualifier
    How to fix error message: “Invalid value [***] for [transl_table] qualifier.”?

  3. Are there really some stop codons in the range of CDS feature because of frame shift, nonsense mutation, or some other reason?

    1. In case of pseudogene
      Click [Select Qualifier] button beside CDS and add /pseudogene qualifier. Then, you can specify /pseudogene qualifier with its controlled vocabularies.
      See also b) considered pseudogene in detail.

    2. In cases of unsure whether it is pseudogene or not, the reason of stop codon is uncertain, or on the process of diversity increasing related to acquired immunity, describe misc_feature, not CDS feature.
      See a) Putative nonsense mutation, frameshift caused by uncertain reason, or on the process of diversity increasing related to acquired immunity for IgG etc. in detail.

  4. In other cases.
    There are some possibilities to output this error because of ribosomal slippage, RNA editing, exceptional amino acid usage, transpon insertion and so on.