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Please add below changes to your code.

You need to add GROUP BY entity_id.

Add select query on collection like below.

$collection->getSelect()->joinLeft(
    array('s' => new Zend_Db_Expr('(SELECT (o.grand_total - o.tax_amount) grand_excl_tax,'
        . ' FROM ' . Mage::getSingleton('core/resource')->getTableName('sales/invoice') . ' AS o'
        . ' GROUP BY entity_id)')),
    "s.entity_id = main_table.entity_id",
    array('grand_excl_tax')
);

After that add filter_index in addColumn:

$this->addColumn('grand_excl_tax', array(
    'header'    => Mage::helper('customer')->__('Amount Excl. Tax'),
    'index'     => 'grand_excl_tax',
    'filter_index' => 's.grand_excl_tax',
    'type'      => 'currency',
    'align'     => 'right',
    'currency'  => 'order_currency_code',
));

I am tested it and it's working fine form me, After applying this there is not any issue on grid filter.

Let me know still if you face any issue.