The sears of T99 and T38 Arasika's have a stud which protrudes up through the receiver bottom as the trigger is to the rear. This stud engages one of two corresponding notches milled onto the bolt body. One of these notches locks the bolt closed when the rifle is fired and the other that prevents the bolt from being closed with the trigger pulled is, I believe, there just for that purpose as Arisaka's don't have any means of being manually cocked without working the bolt.
Any Arisaka 38 or 99 that allows the bolt to be closed with the trigger held back has a broken or modified sear and should be repaired before firing. The only way to de-cock an Arisaka is to dry fire it, that's how they were designed.