How to filter groups of paired values in Views
I am not able to reproduce the behavior you describe. In configuring a Field Collections and Views in the way you describe I do get the desired results.

Here is a screenshot of my configuration:



And here are the results:



And here is the filtering:

By letter:



By number:



Mismatched letter/number yields no results:



And here is the full View export:

$view = new view();
$view-&gt;name = 'stacktest_fieldcollection';
$view-&gt;description = '';
$view-&gt;tag = 'default';
$view-&gt;base_table = 'node';
$view-&gt;human_name = 'stacktest_fieldcollection';
$view-&gt;core = 7;
$view-&gt;api_version = '3.0';
$view-&gt;disabled = FALSE; /* Edit this to true to make a default view disabled initially */

/* Display: Master */
$handler = $view-&gt;new_display('default', 'Master', 'default');
$handler-&gt;display-&gt;display_options['title'] = 'stacktest_fieldcollection';
$handler-&gt;display-&gt;display_options['use_more_always'] = FALSE;
$handler-&gt;display-&gt;display_options['access']['type'] = 'perm';
$handler-&gt;display-&gt;display_options['cache']['type'] = 'none';
$handler-&gt;display-&gt;display_options['query']['type'] = 'views_query';
$handler-&gt;display-&gt;display_options['exposed_form']['type'] = 'basic';
$handler-&gt;display-&gt;display_options['pager']['type'] = 'full';
$handler-&gt;display-&gt;display_options['pager']['options']['items_per_page'] = '10';
$handler-&gt;display-&gt;display_options['style_plugin'] = 'table';
/* Relationship: Content: FC (field_fc) */
$handler-&gt;display-&gt;display_options['relationships']['field_fc_value']['id'] = 'field_fc_value';
$handler-&gt;display-&gt;display_options['relationships']['field_fc_value']['table'] = 'field_data_field_fc';
$handler-&gt;display-&gt;display_options['relationships']['field_fc_value']['field'] = 'field_fc_value';
$handler-&gt;display-&gt;display_options['relationships']['field_fc_value']['required'] = TRUE;
$handler-&gt;display-&gt;display_options['relationships']['field_fc_value']['delta'] = '-1';
/* Field: Content: Title */
$handler-&gt;display-&gt;display_options['fields']['title']['id'] = 'title';
$handler-&gt;display-&gt;display_options['fields']['title']['table'] = 'node';
$handler-&gt;display-&gt;display_options['fields']['title']['field'] = 'title';
$handler-&gt;display-&gt;display_options['fields']['title']['alter']['word_boundary'] = FALSE;
$handler-&gt;display-&gt;display_options['fields']['title']['alter']['ellipsis'] = FALSE;
/* Field: Field collection item: Letter */
$handler-&gt;display-&gt;display_options['fields']['field_letter']['id'] = 'field_letter';
$handler-&gt;display-&gt;display_options['fields']['field_letter']['table'] = 'field_data_field_letter';
$handler-&gt;display-&gt;display_options['fields']['field_letter']['field'] = 'field_letter';
$handler-&gt;display-&gt;display_options['fields']['field_letter']['relationship'] = 'field_fc_value';
/* Field: Field collection item: Number */
$handler-&gt;display-&gt;display_options['fields']['field_number']['id'] = 'field_number';
$handler-&gt;display-&gt;display_options['fields']['field_number']['table'] = 'field_data_field_number';
$handler-&gt;display-&gt;display_options['fields']['field_number']['field'] = 'field_number';
$handler-&gt;display-&gt;display_options['fields']['field_number']['relationship'] = 'field_fc_value';
/* Sort criterion: Content: Post date */
$handler-&gt;display-&gt;display_options['sorts']['created']['id'] = 'created';
$handler-&gt;display-&gt;display_options['sorts']['created']['table'] = 'node';
$handler-&gt;display-&gt;display_options['sorts']['created']['field'] = 'created';
/* Contextual filter: Field collection item: Letter (field_letter) */
$handler-&gt;display-&gt;display_options['arguments']['field_letter_value']['id'] = 'field_letter_value';
$handler-&gt;display-&gt;display_options['arguments']['field_letter_value']['table'] = 'field_data_field_letter';
$handler-&gt;display-&gt;display_options['arguments']['field_letter_value']['field'] = 'field_letter_value';
$handler-&gt;display-&gt;display_options['arguments']['field_letter_value']['relationship'] = 'field_fc_value';
$handler-&gt;display-&gt;display_options['arguments']['field_letter_value']['default_argument_type'] = 'fixed';
$handler-&gt;display-&gt;display_options['arguments']['field_letter_value']['summary']['number_of_records'] = '0';
$handler-&gt;display-&gt;display_options['arguments']['field_letter_value']['summary']['format'] = 'default_summary';
$handler-&gt;display-&gt;display_options['arguments']['field_letter_value']['summary_options']['items_per_page'] = '25';
$handler-&gt;display-&gt;display_options['arguments']['field_letter_value']['limit'] = '0';
/* Contextual filter: Field collection item: Number (field_number) */
$handler-&gt;display-&gt;display_options['arguments']['field_number_value']['id'] = 'field_number_value';
$handler-&gt;display-&gt;display_options['arguments']['field_number_value']['table'] = 'field_data_field_number';
$handler-&gt;display-&gt;display_options['arguments']['field_number_value']['field'] = 'field_number_value';
$handler-&gt;display-&gt;display_options['arguments']['field_number_value']['relationship'] = 'field_fc_value';
$handler-&gt;display-&gt;display_options['arguments']['field_number_value']['default_argument_type'] = 'fixed';
$handler-&gt;display-&gt;display_options['arguments']['field_number_value']['summary']['number_of_records'] = '0';
$handler-&gt;display-&gt;display_options['arguments']['field_number_value']['summary']['format'] = 'default_summary';
$handler-&gt;display-&gt;display_options['arguments']['field_number_value']['summary_options']['items_per_page'] = '25';
$handler-&gt;display-&gt;display_options['arguments']['field_number_value']['limit'] = '0';
/* Filter criterion: Content: Published */
$handler-&gt;display-&gt;display_options['filters']['status']['id'] = 'status';
$handler-&gt;display-&gt;display_options['filters']['status']['table'] = 'node';
$handler-&gt;display-&gt;display_options['filters']['status']['field'] = 'status';
$handler-&gt;display-&gt;display_options['filters']['status']['value'] = 1;
$handler-&gt;display-&gt;display_options['filters']['status']['group'] = 1;
$handler-&gt;display-&gt;display_options['filters']['status']['expose']['operator'] = FALSE;

/* Display: Page */
$handler = $view-&gt;new_display('page', 'Page', 'page');
$handler-&gt;display-&gt;display_options['path'] = 'stacktest-fieldcollection';