I keep falling into this trap. We use SQL Server 2008 and if there's one thing it can't tolerate is using comments and parameters in the same SQL query inside SSIS.

When compiling the queries to send to the Server it seems to get rid of newlines while processing the parameters. The result is:
FROM [NameTable] --Comment
WHERE [id] = ?

FROM [NameTable] --CommentWHERE [id] = ?

Multiline comment blocks seem to work ok, presumably because they have a closing */

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