but ali told the police that spencer was loyal to her as far as she knew and said that they never spoke of the pills again.
Are you talking about something specific I said? maybe something I said about her polygraph test?
If not, let me know, but I'll just answer assuming it is :)
We now know Holbrook was working for Alison, which means her entire interview was set up before, including every question. That's why he didn't ask anything about her and Bethany, or barely anything about her in general.
The entire interview was focused on Spencer, and she made a point in emphasizing that Spencer followed her to the Dilaurentis house, which isn't true, and that she was on pills and alcohol during that time frame. They never spoke of the pills again because Alison was gone after that. Alison needed a escape goat, and Spencer was exactly that. The interview was what gave the police motive to arrest Spencer, and Alison knew that could and most likely would happen, and that's why she convinced Holbrook to only ask those questions.