Check that the battery has the correct polarity (+ should be red wire, - should be black wire). There is no standard for how to wire the JST connectors and so some packs have them a different way round
The board has a reverse voltage protection circuit to prevent you accidentally frying things if you use a pack wired the wrong way. If your pack is the wrong way round then you can very carefully, with sharp tweezers, lift the little retaining bit of plastic on the JST plug and gently pull each contact out (no force required with the plastic arm lifted), then put them back in the right way round (they’ll snap in). CAREFUL though, because touching them together unintentionally will result in sparks.
As @smittytone says, also check the jumper settings. By default, 006 breakout is not jumpered for Li-Ion power. Jumper settings are on the back of the PCB for reference.