They rebuilt the line from scratch back in 1995 and they probably figured that they could save money by only building the second track at Botanic Gardens. They figured that since the shuttle runs every 10 minutes, they can time it so that trains pass each other at Botanic Gardens and don't need to double track the whole route.
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''Bingo. DeKalb Avenue''

Conductor on a Brooklyn-bound B train. 2004