筋が通る is a set idiom 'logic passes through' = 'to make sense, to be coherent.' ~ていない on this state verb marks the ongoing condition of not-making-sense. わけじゃない ('it's not the case that ~') is the softening denial pattern used to push back against an assumption or implication, rather than denying a fact outright. The speaker is rebutting an accusation by reframing what did or didn't happen.