Your query is enumerating (indirectly) through the rows in the table. As you should already know, you cannot modify a collection (remove something in this case) as you enumerate over it. Throw the contents into a list beforehand. That way you're not enumerating through the actual table but a copy of some rows.
var query = (from row in errorDataSet.Tables.AsEnumerable() where !String.IsNullOrEmpty(row.Field<string>("Message")) select row).ToList();
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