'"Data science" ends up with a bloody neck from Occam's razor.'
Heh, I like the imagery. I wouldn't really call it Data Science with capital letters either. It's just plain-old exploratory analysis.
I wouldn't say the hypothesis is convoluted, especially since we see bizarre data coming out of Caltrain API at times, and experience has taught us to distrust our instruments when observing strong systematic bias. But single-tracking due to construction IS obviously a better explanation... because it's probably true.
What is still confusing is that the train is delayed several minutes, but then recovers at the very next station. That is odd behavior for a train to 'make up' that much time so quickly. Typical behavior is just to keep getting later.
Or maybe Occam will strike again in the comments with an obviously correct explanation!