Hi Naren
Are you using mongoexport with the "feilds" option, that should stop the missalignment on missing fields, if it does not then it is a bug and you should report it on JIRA
--fields <field1[,field2]>, -f <field1[,field2]>
Specifies a field or fields to include in the export. Use a comma separated list of fields to specify multiple fields.
For csv output formats, mongoexport includes only the specified field(s), and the specified field(s) can be a field within a sub-document.
For JSON output formats, mongoexport includes only the specified field(s) and the _id field, and if the specified field(s) is a field within a sub-document, the mongoexport includes the sub-document with all its fields, not just the specified field within the document.
--fieldFile <filename>
An alternative to --fields. The --fieldFile option allows you to specify in a file the field or fields to include in the export and is only valid with the --type option with value csv. The file must have only one field per line, and the line(s) must end with the LF character (0x0A).
mongoexport includes only the specified field(s). The specified field(s) can be a field within a sub-document.
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