The boss says that Sam was left out of the game because of an internal issue.
The Baggies were able to have him back after he had completed a three-match ban.
Ismael said that the three caps player would not be considered for the Millwall game.
David Button was in goal for Albion.
The loss was the Baggies first in the league at The Hawthorns this season and leaves them fifth in the table, seven points off the automatic promotion places.
After starting all 24 of his side's Championship games this season, he was dismissed after the final whistle.
Ismael told the radio station that there was an issue with his keeper and he was not in the squad for the game.
He won't be in the squad on Saturday because of that, but he will be back after that.
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