This is still more than it should cost, but it's important to have the facts straight.
The larger answer to the MTA's financial mess is multitudinous:
1. It's really 5+ independent transport systems folded into one big, unwieldy authority. Some of those systems (particularly the LIRR and MNRR, but not NYCT) are famous for overtime fraud[1].
2. NYCT runs 24/7, which means that maintenance operations need to happen at night or other overtime periods. That means higher baseline costs for labor.
3. The MTA intentionally under-hires, under the financial theory that overtime pay is more sustainable than more heads on the 20-year pension pipeline.
4. Any amount of capital development on the subway is fundamentally expensive, both due to the age of the system, the complexity of the infrastructure that's developed around it, the need to minimize disruption to the rest of the system and city, etc. The MTA has repeatedly opted for bigger, more expensive capital programs that minimize disruption throughout the city, with the SAS's extremely deep tunnels being a good example of this.
[1]: https://www.justice.gov/usao-sdny/pr/highest-paid-mta-employ...