Indexing hangs at "Initializing"

Sometimes indexing hangs at "initializing" after restarting indexing that stopped for some error.

The php cpu usage jumps to 100%, and the mysql db has some sleeping query that hangs as well. When I kill that query I get a long error message like this:
Unsure why Search API is trying to select a revision when I dont have any revisions selected in the Fields section.

I will try to collect more info why this happens. I wonder if I may have a malformed entity somewhere that causes this.

Indexing a maximum number of 3675720 items (50 items per batch run)  [ok]
for the index Test.
exception 'PDOException' with message 'SQLSTATE[HY000]: General      [error]
error: 2006 MySQL server has gone away' in
..../includes/database/database.inc:2171
Stack trace:
#0 ..../includes/database/database.inc(2171):
PDOStatement->execute(Array)
#1 ..../includes/database/database.inc(683):
DatabaseStatementBase->execute(Array, Array)
#2 ..../includes/database/select.inc(1265):
DatabaseConnection->query('SELECT revision...', Array, Array)
#3 ..../includes/entity.inc(198):
SelectQuery->execute()
#4 ..../includes/common.inc(7919):
DrupalDefaultEntityController->load(Array, Array)
#5
..../sites/all/modules/entity/includes/entity.wrapper.inc(7                                                                                                                                                             15):
entity_load('commerce_produc...', Array)
#6
..../sites/all/modules/search_api/search_api.module(2217):
EntityDrupalWrapper->value(Array)
#7
..../sites/all/modules/search_api/includes/index_entity.inc                                                                                                                                                             (499):
search_api_extract_fields(Object(EntityDrupalWrapper), Array)
#8
..../sites/all/modules/search_api/search_api.module(1531):
SearchApiIndex->index(Array)
#9
..../sites/all/modules/search_api/search_api.module(1487):
search_api_index_specific_items(Object(SearchApiIndex), Array)
#10
..../sites/all/modules/search_api/search_api.module(2969):
search_api_index_items(Object(SearchApiIndex), '50')
#11 [internal function]:
_search_api_batch_indexing_callback(Object(SearchApiIndex), '50',
3990598, true, Object(DrushBatchContext))
#12 /usr/local/src/drush/commands/core/drupal/batch.inc(149):
call_user_func_array('_search_api_bat...', Array)
#13 /usr/local/src/drush/commands/core/drupal/batch.inc(101):
_drush_batch_worker()
#14 /usr/local/src/drush/includes/batch.inc(90):
_drush_batch_command('2700')
#15 /usr/local/src/drush/commands/core/core.drush.inc(1168):
drush_batch_command('2700')
#16 [internal function]: drush_core_batch_process('2700', '2700')
#17 /usr/local/src/drush/includes/command.inc(368):
call_user_func_array('drush_core_batc...', Array)
#18 /usr/local/src/drush/includes/command.inc(219):
_drush_invoke_hooks(Array, Array)
#19 [internal function]: drush_command('2700', '2700')
#20 /usr/local/src/drush/includes/command.inc(187):
call_user_func_array('drush_command', Array)
#21 /usr/local/src/drush/lib/Drush/Boot/BaseBoot.php(62):
drush_dispatch(Array)
#22 /usr/local/src/drush/drush.php(70):
Drush\Boot\BaseBoot->bootstrap_and_dispatch()
#23 /usr/local/src/drush/drush.php(11): drush_main()
#24 {main}
The external command could not be executed due to an application     [error]
error.