I've been riding Caltrain for close to a year, taking my bike onboard as part of my daily commute to work. A majority of the time, Caltrain operates smoothly without delay. However, it isn't unheard of for Caltrain to have "incidents" that cause delays or changes to the schedule.
Sadly, the most common reason for delay is when a trespasser on the tracks is hit and often times killed. It is also the situation that causes the longest delays (between 1-4 hour delay depending on how far you are from the incident) because the police must determine if it was a suicide or murder. Additionally, Caltrain conductors are not given information in the cause, but can often be found on Twitter. In my experience, the conductors onboard may ask everyone to deboard (and wait for a bus bridge that bypasses the station) or inform everyone the train is turning around (and you can head back to your start destination). The situation is chaotic and confusing. Because the conductors leave with the trains, there isn't a Caltrain representative available to get information about the bus bridge (ETA). From my experience, if I am close (a station or two away from the incident), trying to catch the next train that single-tracks past the incident is often times the easiest least stressful option. It guarantees I have a seat on the next train going southbound, and I can just wait onboard in a temperature controlled train. If I take the bus bridge, I have to fight (peacefully) with other bus riders and passengers already waiting at the station. In most cases, the train schedule changes and stops at every stop.
Other less minor (and less time delay) Caltrain incidents include mechanical problems where the train's engine continues to run, but the lights, temperature control (AC and Heat), and intercom are disabled. Usually, they can do a quick restart which gets the train back up and running within 10 minutes.
All in all, delays due to incidents can be inconvenient. But like any public service, unexpected problems can occur. Just don't panic and deal with the situation. If there is something you don't like, tell Caltrain how you would handle the incident. All in all, I still love the service Caltrain runs and will be taking it as long as it works for me.