Production may not have wanted to let the extras break so they wouldn’t need to wrangle everybody together once filming was ready to go, but things got delayed and took longer than expected.
It seems like this may have been just an attempt at getting some quick shots that took much longer than expected.
Based on the report it sounds like this scene only involved extras, there’s no mention of Joaquin Phoenix or other actors being involved.
This was likely just being done to get shots of people on a subway as part of a larger sequence that will be edited together.