A Tower Local Control trainee reported they instructed an aircraft to line up and wait before the preceding aircraft began its takeoff roll.

Narrative

I was training on Local Controller 1. The configuration during the event was [traffic landing and departing east] and we were Call for Release by TRACON. I called Clearance 1 for releases on Aircraft X and Aircraft Y; and was told to hold. After some time; I accepted a handoff for an arrival. When the arrival was around a 10 mile final; I was given releases for both Aircraft X and Aircraft Y. I immediately told Aircraft X cleared for takeoff; and soon after told Aircraft Y to line up and wait. I was anticipating that there would be enough separation between Aircraft X starting takeoff roll and Aircraft Y proceeding on the runway to line up and wait. However; Aircraft X still was not in position and Aircraft Y was following Aircraft X onto the runway. Once I noticed Aircraft Y was following Aircraft X onto the runway; I asked my Trainer what to do. He then keyed up and told Aircraft Y to hold position. The pilot replied that they were past the hold short line; and my Trainer repeated to hold position and cancel line up and wait. A recommendation I would have to prevent the re-occurrence of this event is to wait longer between clearing an aircraft for takeoff if they are behind the hold short line and telling the second aircraft in line to line up and wait; to ensure that the first aircraft has started takeoff roll. I think because Aircraft X was being held by TRACON for a while; they were not ready to get onto the runway immediately when I cleared them for takeoff. Another recommendation is to scan better; because if I had scanned and saw the first aircraft wasn't in position yet I would not have told the second aircraft to line up and wait. The last recommendation I have is to be careful with expectation bias. I was anticipating and expecting that Aircraft Y would wait until Aircraft X had started takeoff roll before starting to line up and wait; but I need to ensure there is enough space in between two aircraft in the same situation in the future.