It is very difficult to search for missing text formats.
Add the text where the format is missing.
In check_markup() replace watchdog('filter', 'Missing text format: %format.', array('%format' => $format_id, WATCHDOG_ALERT); with watchdog('filter', 'Missing text format: %format in %text.', array('%format' => $format_id, '%text' => $text), WATCHDOG_ALERT);.
This improves root cause for missing text formats.
Active
7.0 ⚰️
Knowing the text passed to check_markup() does not help to know why the code calling it is using a format that does not exist, nor why that format does not exist. It could help to understand which line caused the error, if the text is a literal string.
What would really help is a back trace.