This was a response to someone who was griping about a situation she didn’t like, even as she recognized the pettiness of her complaint. It is a mash of “bone to pick” (grounds for a complaint or dispute) and “truth in (of) the matter” (used when you want to show you are being honest). Perhaps the speaker was thinking about the marrow in the bone, the “matter” inside the bone. A big thanks to curioussteph for uttering this one, realizing it was a malaphor, and sending it in.
If you want to get to the matter of malaphors, look no further than my book “He Smokes Like a Fish and other Malaphors”, available on Amazon at https://www.amazon.com/dp/0692652205. No bones to pick there!