This isn't about physics. It's about super old poorly working schedules. Again, it shouldn't take 60 plus minutes to go 40 miles with only 2 stops. Or 90 minutes, with a transfer that you pray happens (at Hicksville), for the same route. A train shouldn't DAILY (when I used HP) pull out of HP, sit for 15 to 20 minutes before then hauling ass to Jamaica.
As to unexplained delays, they take place all the time. You may know, the crew may know, dispatchers may know what they are. But passengers don't in many cases. All they know is that on a good day it takes a lot longer to get in to work, and get home from work than it should, and with frequent 'equipment problems, there are a lot of days that are not good. There are reasons why LIRR gets nicknames like Fail Road, Snail Road, Hell Road, etc. Locos constantly breaking down. Doors breaking. Signal systems, even brand new ones, breaking. Switches breaking. If they weren't, I wouldn't get the stream of emails I get some mornings or evenings about delays.
Add to that, if you also need the subway, to it's constant breakdowns and 'congestion ahead' announcements. The L, which has a modern signal system, has frequent breakdowns. As I recall, the 7 does as well, with frequent breakdowns.