OP's situation happens quite a lot for me. I have a monthly tix, and in certain stations / turnstile, it won't get through, almost always. I believe it's a combo of bad reader and card. Just keep trying or talk to the agent.
And don't try the emergency door even if your card doesn't work. I have a friend who did that, got a $150 ticket. They don't arrest you, they just fine you even if you have a pass with you. So, always talk to agent first.