No, the boot drive does not count. However anything like another USB drive or a card reader does count. If there is nothing obvious at your end then it might be a case of looking through the diagnostics carefully to see exactly what drives are being seen by Unraid to identify the culprit.
The commonest mistake is to leave a removable drive plugged in (or a spare drive)) which if present at array start time DOES count, although once the array is started such drives can be plugged in without invoking the device limit check.