I dared to open the issue here because the community should be aware of the problem I faced when deleting several hundreds of nodes using Drupal's standard content management interface. However, the problem most probably comes from database server, not Drupal, since there were no warnings/errors coming from database layer.
Pre-conditions:
1. A rather loaded (production) MySQL server (5.5.30-30.2-log). It's hard to say how loaded the server should be,
but the higher is load - the better.
2. Several hundreds of nodes with various fields (the more fields - the better)
Steps:
1. Open admin/content and all of the pages that list contents (one browser tab - one page).
2. Select all of the nodes on all of the pages and click "Delete selected content".
3. Go through each tab and confirm deletion. That will run X bulk deletion requests in parallel.
Expected result:
1. All of the nodes are deleted (node table is empty).
2. All content type field tables (field_data_field) and revision tables (field_revision_field) do not have any records.
Actual result:
1. All of the nodes are deleted (node table is empty).
2. NOT all content type field tables (field_data_field) and revision tables (field_revision_field) are empty, some of them still have records attached to a non-existent node.
The issue was also reproduced with delete_all module (with safe and long deletion method selected).