So ya i have narrowed the problem down and can see that when i make my model stop for 3 seconds in order to perform an animation the rigidbody stops responding to collision, and when the GO starts moving again collision works as intended. The rigidbody is set it isKinematic and the collider projectiles have a trigger collider on them. NOTE the problem still exists if i switch the rigidbody to no isKinematic.
It sounds like your rigidbody is falling asleep. See the docs. You would use rigidbody.WakeUp(); to prevent this from being a problem.
If that isn't it, then it could well have something to do with either your exact setup or what you are expecting it to do. In that case, perhaps you might consider detailing clearly what you are doing to test your collisions when your Rigidbody is stopped and how exactly you expect it to react.