It's not only the BMT that poorly plans their system, your forgetting the IRT. The infamous Rogers Junction is clear example of that poor planning. As for the IND's planning, they're usually smart about their development. Their shortsightedness was mainly do to financial issues as well as WWII being a thing. If it wasn't for either of them, we would probably be seeing more of the Second System like the SAS and whatever else the IND wanted to build.
Infrastructure-wise, if you can call the post-unification system “IND” then some of the more poorly done jobs would be:
The Chrystie Street connector
Look no further than last month’s weekend service changes for supporting evidence.
The 36 Street connector connecting 63 Street to Queens Boulevard
Took away much of the trackage for train storage, making it only useful for half-length trains. Arguably, storage tracks aren’t that useful from a passenger’s perspective anyway.
The Archer Avenue extension
No connection between upper and lower levels means that when one level is taken out of service for construction work, its associated routes are truncated instead of being routed to the other level.
Pre-unification, these would be great examples of poor planning on the IND’s part:
Court Street
Dead-ends in Brooklyn.
World Trade Center
No tail tracks.
145 Street as a terminal for local trains
Though to their credit, they probably never intended 145 Street to be a regular terminal—only Bedford Park Boulevard.