London has existed for over a thousand years. It has just grown organically. All recent services (such luxuries as underground, trains, ringroads, mains water, electricity, sewers, communication lines) have been retrofitted on that base -- and it shows. The roads are the wrong size for the amount of traffic -- trains clash and are overfull, high rise offices are planned but foundations have to carefully avoid all the tunneling below.
New York, in it's current form, is a lot younger than that. A lot of the concepts "we might want sewers" / electricity / rail, to some extend, could be taken into account when the city grid was being laid out. It's a lot easier to build sewers / underground trains before high rise buildings have gone up on top.
Back to the software world -- if you've got code that was pre-Web / pre-Internet but needs to be brought into the 21st century, inevitably things won't fit. I've worked on some banking code which had punchcard assumptions shine through. Some of that code is 40 years old. You could call it crufty, some would call it rock-solid.
I've written code that computes a CRC. It's been done before. The naive/reference implementation works but isn't fast. The optimized version, and how the heck that came about from the naive implementation to those magic few lines of code, looks nothing like it. Now rather than you glazing over "what the?", I figure that *if* you have to overhaul this code, you'd like to know *why* this code looks like it does. So I explained why. In the code. In a full page of comments.
A lot of "real world" code out there has not been designed, it has grown, and that's part of the problem. Think of cities that have grown (London?) rather than be designed according to some grand master plan (New York?) and major reengineering exercises need to be undertaken (in the case of London, as one example, sewage pipes were fitted in underneath). Inevitably there's some shortcuts taken or real reasons that you could not quite do the best job.
Codewise, the oldest running code probably lives in the banking system or the telephony system. Typically code that has grown over time and can't just be shut down for an upgrade -- "what do you mean close the bank for a week?". Now whatever code runs there has been kept running (bodged?) for decades, but pretty it probably isn't.
When all else fails, read the instructions.