https://api.drupal.org/api/drupal/core%21lib%21Drupal%21Core%21Entity%21...
The documentation here says that "The size of the conditional is the size of its conditional array minus one, because one element is the conjunction." After getting some unexpected results though I stepped through the code and found that the conjunction is not in the conditions array that the count function is going through (please see screenshot).
As such to get the expected results we had to use the conditions() function to get the array of conditions and pass them through count() ourselves.