Because of the R44s' earlier than planned retirement (except the Staten Island Railway cars) and the R32s and R42s assigned to services utilizing eight-car trains at the time, the setup was reversed, with the majority of the R179s being arranged in four-car sets.

Because of manufacturing defects during the construction process, the timeline for delivery was pushed back two years, and the cost of the contract rose to $735 million.

[6]: 11  The R179s were also the last subway car order to be built by Bombardier Transportation prior to being acquired by Alstom in January 2021.

[9] The R179s, like the R160s, employ an advanced alternative to electronic strip maps called the "Flexible Information and Notice Display" ("FIND"), which are manufactured by Axion Technologies Ltd.

Communication-based train control (CBTC) equipment will be installed in all R179s that are already on MTA property,[15] in conjunction with the ongoing automation of B Division lines.

This feature was previously tested on R160A set 9798–9802 and has been implemented on other trains as a part of a plan to fix the subway's 2017 state of emergency.

The R179s also have larger picture windows, resulting in a tighter cab for the conductors and train operators, since slightly more space was required to accommodate the HVACs.

[17] Later, in the 2010–2014 Capital Program, the proposed order was expanded to 420 cars (340 for the New York City Subway and 80 for the Staten Island Railway).

[32] The R179s were originally intended to replace all the R44s, but due to structural integrity issues found on New York City Transit's R44s in late 2009, those cars' retirement was facilitated by an option order of R160s.

Additionally, the Metropolitan Transportation Authority later dropped the plan to order R179s for the Staten Island Railway, instead opting to overhaul some R46s to replace the existing R44s there (which has also since been canceled).

[34] Some R32s were expected to be retained due to delays in the delivery of the R179s and the potential need for extra rolling stock to provide additional service.

However, as NYCTA's and Bombardier's inspectors found cracks due to welding issues in the prototype train's chassis, the entire lot was rejected, and the delivery schedule was pushed back by two years.

[41] In addition, because of the 2-year delay in producing the R179s, Bombardier was banned from bidding on the R211 contract, which would replace other older B Division rolling stock.

The next five cars (3015–3019) were delayed and were delivered between November 15 and 17, 2016, forming a complete pilot ten-car train for acceptance testing and evaluation.

[54][55][56] After successful completion, the four-car R179 sets officially entered revenue service on December 27, 2017, a month later than originally planned.

[57][58] The pilot five-car R179 sets underwent specification modifications at Bombardier's Kanona Facility in summer 2018 and were re-delivered for further testing.

[59] By the start of December 2018, some trains had to be taken out of service due to manufacturing defects such as doors, propulsion, and air compressors issues.

[70] Aside from the door issues, the Transport Workers Union of America has complained about problems with operating the R179, such as stiff windows, slippery controls, and other design flaws.

On June 3, 2020, a set of R179s running on the A train had its link bar separated between the sixth and seventh cars while in service at Chambers Street station, causing the consist to be split into two.

[73][74][75][76] The entire fleet was subsequently pulled from service and underwent thorough safety investigations to address any in-service issues that do occur.